151
|
Jiang F, Wu Z, Zheng Y, Frana TS, Sahin O, Zhang Q, Li G. Genotypes and Antimicrobial Susceptibility Profiles of Hemolytic Escherichia coli from Diarrheic Piglets. Foodborne Pathog Dis 2019; 16:94-103. [PMID: 30688527 DOI: 10.1089/fpd.2018.2480] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hemolytic Escherichia coli are important pathogens in neonatal and weaned pigs. In this study, we analyzed 95 hemolytic E. coli isolated from intestinal contents or fecal samples of diarrheic piglets in 15 states of the United States between November 2013 and December 2014. Phenotypic antimicrobial susceptibility was determined through Sensititre BOFO6F plates for all the strains. They were all resistant to clindamycin, penicillin, tiamulin, tilmicosin, and highly resistant to oxytetracycline (91.6%), chlortetracycline (78.9%), ampicillin (75.8%), and sulfadimethoxine (68.4%). 86.2% of them were multidrug resistant. Whole genome sequencing (WGS) showed that 55 strains were enterotoxigenic E. coli (ETEC) and 40 strains were non-ETEC, and the strains belonged to 22 known and 2 novel sequence types (STs). ST100 and ST10 were the main and predominant STs in ETEC strains, whereas the non-ETEC strains were diverse with ST23 and ST761 as the main STs. Antibiotic resistance gene/mutation profiling of the genomes confirmed the results of antimicrobial susceptibility test. Notably, significant differences were found in the susceptibility to enrofloxacin between ETEC and non-ETEC (58.2% vs. 5.0%) and gentamicin (32.7% vs. 7.5%). ampH, ampC2, and ampC1 were the most common beta-lactamase genes in all E. coli strains, and extended-spectrum beta-lactamase (ESBL) genes were rare in these isolates. This study provides new insights into antibiotic resistance and genotypes of intestinal pathogenic E. coli associated with swine disease in the United States, and support the utility of WGS in accurate prediction of resistance to most antibiotics.
Collapse
Affiliation(s)
- Fengwei Jiang
- 1 Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,2 Department of Veterinary Diagnostic and Production Animal Medicine and College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Zuowei Wu
- 3 Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Ying Zheng
- 2 Department of Veterinary Diagnostic and Production Animal Medicine and College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Timothy S Frana
- 2 Department of Veterinary Diagnostic and Production Animal Medicine and College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Orhan Sahin
- 2 Department of Veterinary Diagnostic and Production Animal Medicine and College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Qijing Zhang
- 3 Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Ganwu Li
- 1 Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,2 Department of Veterinary Diagnostic and Production Animal Medicine and College of Veterinary Medicine, Iowa State University, Ames, Iowa
| |
Collapse
|
152
|
Nabti LZ, Sahli F, Radji N, Mezaghcha W, Semara L, Aberkane S, Lounnas M, Solassol J, Didelot MN, Jean-Pierre H, Dumont Y, Godreuil S. High Prevalence of Multidrug-Resistant Escherichia coli in Urine Samples from Inpatients and Outpatients at a Tertiary Care Hospital in Sétif, Algeria. Microb Drug Resist 2019; 25:386-393. [PMID: 30676258 DOI: 10.1089/mdr.2018.0314] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The worldwide dissemination of multidrug-resistant (MDR) Enterobacteriaceae is a major public health issue. The aim of this study was to investigate the prevalence of MDR Escherichia coli (MDR-EC) isolates, in inpatients/outpatients with urinary tract infections at Sétif University Hospital (Algeria). Bacterial cultures were obtained from 426 of the 3,944 urine samples collected from January 2015 to February 2017. Among these cultures, 215 E. coli isolates were identified by mass spectrometry, and 38 (17.7%) were MDR-EC (disk diffusion method): 36 produced only extended-spectrum β-lactamases (ESBL), one ESBL and a carbapenemase, and one only a cephalosporinase (double-disk synergy test). Multiplex PCR and sequencing analyses showed that 37 ESBL-producing isolates harbored genes encoding CTX-M enzymes (CTX-M-15 in 33 isolates, 89.19%; and CTX-M-14 group in four isolates, 10.81%). One CTX-M-15-producing isolate co-expressed also an OXA-48-like carbapenemase. Phylogenetic group analysis of the 37 ESBL-producing and 178 non-ESBL-producing isolates indicated that the most common phylogenetic group was B2 (54.05% of ESBL-producing and 48.31% of non-ESBL-producing isolates), followed by A and D for ESBL-, and by B1, A, and F for non-ESBL-producing isolates. This is the first report highlighting the presence of MDR-EC isolates that produce both CTX-M and OXA-48-like enzymes in Sétif, Algeria.
Collapse
Affiliation(s)
- Larbi Zakaria Nabti
- 1 Laboratoire de Valorisation des Ressources Biologiques et Naturelles, FSNV, Université de Sétif 1, Sétif, Algérie.,2 Département des Sciences Naturelles, École Normale Supérieure Assia Djebar, Constantine, Algérie
| | - Farida Sahli
- 1 Laboratoire de Valorisation des Ressources Biologiques et Naturelles, FSNV, Université de Sétif 1, Sétif, Algérie.,3 Faculté de Médecine, Université de Sétif 1, Sétif, Algérie.,4 Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU) de Sétif, Sétif, Algérie
| | - Nadia Radji
- 3 Faculté de Médecine, Université de Sétif 1, Sétif, Algérie.,4 Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU) de Sétif, Sétif, Algérie
| | - Wahiba Mezaghcha
- 3 Faculté de Médecine, Université de Sétif 1, Sétif, Algérie.,4 Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU) de Sétif, Sétif, Algérie
| | - Lounis Semara
- 1 Laboratoire de Valorisation des Ressources Biologiques et Naturelles, FSNV, Université de Sétif 1, Sétif, Algérie
| | - Salim Aberkane
- 5 CHU de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France.,6 UMR MIVEGEC IRD-CNRS-Université de Montpellier, IRD, Montpellier, France
| | - Manon Lounnas
- 5 CHU de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France.,6 UMR MIVEGEC IRD-CNRS-Université de Montpellier, IRD, Montpellier, France
| | - Jérôme Solassol
- 7 Département Bio-pathologie cellulaire et tissulaire des tumeurs, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Marie-Noelle Didelot
- 5 CHU de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France
| | - Hélène Jean-Pierre
- 5 CHU de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France.,6 UMR MIVEGEC IRD-CNRS-Université de Montpellier, IRD, Montpellier, France
| | - Yann Dumont
- 5 CHU de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France.,6 UMR MIVEGEC IRD-CNRS-Université de Montpellier, IRD, Montpellier, France
| | - Sylvain Godreuil
- 5 CHU de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France.,6 UMR MIVEGEC IRD-CNRS-Université de Montpellier, IRD, Montpellier, France
| |
Collapse
|
153
|
Lagoutte P, Lugari A, Elie C, Potisopon S, Donnat S, Mignon C, Mariano N, Troesch A, Werle B, Stadthagen G. Combination of ribosome display and next generation sequencing as a powerful method for identification of affibody binders against β-lactamase CTX-M15. N Biotechnol 2019; 50:60-69. [PMID: 30634000 DOI: 10.1016/j.nbt.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 01/15/2023]
Abstract
CTX-M15 is one of the most widespread, extended spectrum β-lactamases, a major determinant of antibiotic resistance representing urgent public health threats, among enterobacterial strains infecting humans and animals. Here we describe the selection of binders to CTX-M15 from a combinatorial affibody library displayed on ribosomes. Upon three increasingly selective ribosome display iterations, selected variants were identified by next generation sequencing (NGS). Nine affibody variants with high relative abundance bearing QRP and QLH amino acid motifs at residues 9-11 were produced and characterized in terms of stability, affinity and specificity. All affibodies were correctly folded, with affinities ranging from 0.04 to 2 μM towards CTX-M15, and successfully recognized CTX-M15 in bacterial lysates, culture supernatants and on whole bacteria. It was further demonstrated that the binding of affibody molecules to CTX-M15 modulated the enzyme's kinetic parameters. This work provides an approach using ribosome display coupled to NGS for the rapid generation of protein ligands of interest in diagnostic and research applications.
Collapse
Affiliation(s)
| | - Adrien Lugari
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Céline Elie
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | | | | | | | | | - Alain Troesch
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Bettina Werle
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France.
| | | |
Collapse
|
154
|
Gwon B, Yoon EJ, Kim D, Lee H, Shin JH, Shin JH, Shin KS, Kim YA, Uh Y, Kim HS, Kim YR, Jeong SH. Differences in Antimicrobial Resistance Phenotypes by the Group of CTX-M Extended-Spectrum β-Lactamase. ANNALS OF CLINICAL MICROBIOLOGY 2019. [DOI: 10.5145/acm.2019.22.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Bareum Gwon
- Department of Clinical Pathology, Sangji University College of Science, Wonju, Korea
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University School of Medicine, Gwangju, Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University Busan Paik Hospital, Busan, Korea
| | - Kyeong Seob Shin
- Department of Laboratory Medicine, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Young Ah Kim
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Young Uh
- Department of Laboratory Medicine, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Young Ree Kim
- Department of Laboratory Medicine, School of Medicine, Jeju National University, Jeju, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
155
|
Xu H, Huo C, Sun Y, Zhou Y, Xiong Y, Zhao Z, Zhou Q, Sha L, Zhang B, Chen Y. Emergence and molecular characterization of multidrug-resistant Klebsiella pneumoniae isolates harboring bla CTX-M-15 extended-spectrum β-lactamases causing ventilator-associated pneumonia in China. Infect Drug Resist 2018; 12:33-43. [PMID: 30588046 PMCID: PMC6304254 DOI: 10.2147/idr.s189494] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background Ventilator-associated pneumonia (VAP) is a common nosocomial infection associated with high morbidity due to multidrug-resistant (MDR) pathogens. The purpose of this study was to determine the occurrence of extended-spectrum β-lactamase (ESBL) genes, especially blaCTX-M-15, in Klebsiella pneumoniae (K. pneumoniae)-associated VAP and to investigate the antimicrobial resistance patterns and molecular epidemiological characteristics of K. pneumoniae strains. Materials and methods From January 2013 to December 2015, we retrospectively collected 89 VAP-causing K. pneumoniae isolates from tertiary-care hospitals in China, among which ESBL-producing strains were assessed for antimicrobial susceptibility. Several antibiotic resistance genes of clinical relevance in K. pneumonia isolates producing ESBL were investigated. Polymerase chain reaction (PCR) and DNA sequencing were employed to characterize the genetic contexts of blaCTX-M-15. Conjugative plasmids carrying blaCTX-M-15 were obtained by mating and further subjected to replicon typing. The genetic relatedness of isolates was assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Results All of the 30 ESBL-producing isolates identified displayed MDR phenotype, with blaSHV, blaCTX-M, blaOXA, and blaTEM detected in 21, 21, 1, and 20 isolates, respectively. blaCTX-M-15 was the most prevalent ESBL gene (19/30, 63.33%), and ISEcp1 was detected 48 bp upstream of 15 blaCTX-M-15 genes. Based on S1-PFGE analyses, 25 isolates exhibited different plasmid profiles, ranging from ~70 to 320 kb. The blaCTX-M-15 with blaTEM and qnr genes and the ISEcp1 element from eight isolates were co-transferrable to recipients via conjugation, with IncFIB, IncFIC, and IncFII being the most prevalent replicons. Twenty different PFGE patterns and 11 sequence types were identified, with ST304 being dominant. Conclusion This work reports the emergence of blaCTX-M-15 in K. pneumoniae-induced VAP in China. We showed that IncFIB, IncFIC, and/or IncFII plasmids carrying blaCTX-M-15 with blaTEM, qnr resistance genes, and the ISEcp1 element mediate the local prevalence in K. pneumoniae-associated VAP.
Collapse
Affiliation(s)
- Hui Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian, China.,Department of Clinical Laboratory, Harbin Medical University Cancer Hospital, Harbin, China
| | - Chunxiu Huo
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China,
| | - Yao Sun
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China,
| | - Yiheng Zhou
- Institute for Chronic and Non-Communicable Disease Prevention and Control, Dalian Center for Disease Prevention and Control, Dalian, China
| | - Yilin Xiong
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China,
| | - Zinan Zhao
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China,
| | - Qi Zhou
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China,
| | - Li Sha
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China,
| | - Beibei Zhang
- Laboratory of Pathogenic Biology, Dalian Medical University, Dalian, China
| | - Yang Chen
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China,
| |
Collapse
|
156
|
Kalsi S, Valiadi M, Turner C, Sutton M, Morgan H. Sample pre-concentration on a digital microfluidic platform for rapid AMR detection in urine. LAB ON A CHIP 2018; 19:168-177. [PMID: 30516215 DOI: 10.1039/c8lc01249k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
There is a growing need for rapid diagnostic methods to support stewardship of antibiotics.
Collapse
Affiliation(s)
- Sumit Kalsi
- Electronics and Computer Science, University of Southampton, Southampton SO17 1BJ, UK.
| | | | | | | | | |
Collapse
|
157
|
Kürekci C, Osek J, Aydın M, Tekeli İO, Kurpas M, Wieczorek K, Sakin F. Evaluation of bulk tank raw milk and raw chicken meat samples as source of ESBL producingEscherichia coliin Turkey: Recent insights. J Food Saf 2018. [DOI: 10.1111/jfs.12605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Cemil Kürekci
- Department of Food Hygiene and Technology, Faculty of Veterinary MedicineHatay Mustafa Kemal University Antakya Hatay Turkey
| | - Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research Institute Pulawy Poland
| | - Muhsin Aydın
- Department of Biology, Faculty of Science and LettersAdıyaman University Adıyaman Turkey
| | - İbrahim Ozan Tekeli
- Department of Pharmacology and Toxicology, Faculty of Veterinary MedicineHatay Mustafa Kemal University Antakya Hatay Turkey
| | - Monika Kurpas
- Department of Hygiene of Food of Animal OriginNational Veterinary Research Institute Pulawy Poland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research Institute Pulawy Poland
| | - Fatih Sakin
- Department of Pharmacology and Toxicology, Faculty of Veterinary MedicineHatay Mustafa Kemal University Antakya Hatay Turkey
| |
Collapse
|
158
|
Kuang D, Zhang J, Xu X, Shi W, Yang X, Su X, Shi X, Meng J. Increase in Ceftriaxone Resistance and Widespread Extended-Spectrum β-Lactamases Genes Among Salmonella enterica from Human and Nonhuman Sources. Foodborne Pathog Dis 2018; 15:770-775. [PMID: 30489150 DOI: 10.1089/fpd.2018.2468] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Salmonella producing β-lactamases has spread rapidly worldwide and poses a serious threat to human and animal health. In this study, we characterized 220 ceftriaxone (CRO)-resistant isolates identified among 3153 Salmonella from humans, animals, food, and water collected in Shanghai, China. They were assessed for antimicrobial susceptibility, phenotypic identification of extended-spectrum β-lactamases (ESBLs), and β-lactamase genes and integrons. CRO resistance in Salmonella increased from 5.0% in 2011 to 8.4% in 2013. Salmonella Enteritidis (45.5%), Salmonella Typhimurium (20.9%) from humans, and Salmonella Indiana (14.5%) from poultry represented the majority of the CRO-resistant isolates. Many isolates were also resistant to other antimicrobials, including nalidixic acid (84.5%), sulfisoxazole (70.5%), and tetracycline (61.8%). Resistance to ciprofloxacin was also found in 33.6% of the isolates. Most isolates (98.2%) were confirmed as ESBL producers. Resistance genes such as blaCTX-M, blaTEM, and blaOXA were detected in 207 (94.1%), 99 (45%), and 53 (24.1%) isolates, respectively. Three types of integron I and one type of integron II were identified in 13 (5.9%) and 2 (0.9%) isolates, respectively. The integrons encompassed 10 different genes: dfrA1/12/17/25, aadA1/2/5, sat2, orfF, and ybeA. Our study underscores concern for increasing CRO resistance, and highlights the widespread ESBL genes in Salmonella enterica.
Collapse
Affiliation(s)
- Dai Kuang
- 1 Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University , Shanghai, China .,2 Joint Institute for Food Safety and Applied Nutrition, University of Maryland , College Park, Maryland.,3 Center for Food Safety and Security Systems, University of Maryland , College Park, Maryland.,4 Department of Nutrition and Food Science, University of Maryland , College Park, Maryland
| | - Jianmin Zhang
- 5 National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University , Guangzhou, China
| | - Xuebin Xu
- 6 Shanghai Municipal Center for Disease Control and Prevention , Shanghai, China
| | - Weimin Shi
- 7 Shanghai Municipal Ke-Ma-Jia Technology Center for Microbiology , Shanghai, China
| | - Xiaowei Yang
- 1 Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University , Shanghai, China
| | - Xudong Su
- 1 Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University , Shanghai, China
| | - Xianming Shi
- 1 Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University , Shanghai, China
| | - Jianghong Meng
- 2 Joint Institute for Food Safety and Applied Nutrition, University of Maryland , College Park, Maryland.,3 Center for Food Safety and Security Systems, University of Maryland , College Park, Maryland.,4 Department of Nutrition and Food Science, University of Maryland , College Park, Maryland
| |
Collapse
|
159
|
Bubpamala J, Khuntayaporn P, Thirapanmethee K, Montakantikul P, Santanirand P, Chomnawang MT. Phenotypic and genotypic characterizations of extended-spectrum beta-lactamase-producing Escherichia coli in Thailand. Infect Drug Resist 2018; 11:2151-2157. [PMID: 30464558 PMCID: PMC6223337 DOI: 10.2147/idr.s174506] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose Extended-spectrum β-lactamases (ESBLs) have become an issue in community worldwide due to an increase in antibiotic resistance over the past decade. This study was aimed to investigate the phenotypic and genotypic characteristics of ESBL-producing Escherichia coli in Thailand. Materials and methods In this study, all clinical isolates collected from tertiary hospitals in Thailand were identified as E. coli by biochemical tests and MALDI-TOF mass spectrometry. ESBL-producing E. coli was preliminary screened with disk diffusion method by cephalosporin disks and confirmed by the method of combination disk diffusion. Antimicrobial susceptibility test was used to determine MIC values of all ESBL-producing E. coli. For genotypic detection, a variety of ESBL genes were determined by PCR. Moreover, multilocus sequence typing (MLST) analysis was performed on internal portions of seven housekeeping genes for the diversity and phylogenetic relatedness of E. coli clonal group. Results Of the 285 ESBL-producing E. coli, most were susceptible to carbapenems. These strains showed a high resistance rate to ciprofloxacin (85.26%). The most frequently detected gene was blaCTX-M1 group at about 71.23% followed by blaCTX-M9 group (38.95%). The blaTEM, blaPER, blaGES, blaVEB, and blaSHV genes were identified in 31.93%, 5.96%, 4.56%, 3.51%, and 0.70% of ESBL-producing isolates, respectively. The bla OXA-10 gene was detected in only one strain. ESBL-producing E. coli isolates with high antimicrobial resistance were further investigated. Among those, E. coli sequence type ST38 was mostly found, followed by ST405, ST410, and ST131. It is noteworthy that the blaCTX-M gene was mainly detected in all four ST-type E. coli clones (ST38, ST405, ST410, and ST131). Conclusion This study provided a recent evidence of the genetic diversity of ESBL-producing E. coli in Thailand. In addition, the profile related to antimicrobial resistance pattern in this region was also demonstrated.
Collapse
Affiliation(s)
- Jiranun Bubpamala
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,
| | - Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,
| | | | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Mullika T Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,
| |
Collapse
|
160
|
Zeynudin A, Pritsch M, Schubert S, Messerer M, Liegl G, Hoelscher M, Belachew T, Wieser A. Prevalence and antibiotic susceptibility pattern of CTX-M type extended-spectrum β-lactamases among clinical isolates of gram-negative bacilli in Jimma, Ethiopia. BMC Infect Dis 2018; 18:524. [PMID: 30342476 PMCID: PMC6196031 DOI: 10.1186/s12879-018-3436-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/05/2018] [Indexed: 12/30/2022] Open
Abstract
Background The prevalence of extended-spectrum β-lactamases (ESBLs) have been reported in clinical isolates obtained from various hospitals in Ethiopia. However, there is no data on the prevalence and antibiotic susceptibility patterns of CTX-M type ESBL produced by Gram-negative bacilli. The aim of this study was to determine the frequency and distribution of the blaCTX-M genes and the susceptibility patterns in ESBL producing clinical isolates of Gram-negative bacilli in Jimma University Specialized Hospital (JUSH), southwest Ethiopia. Methods A total of 224 non-duplicate and pure isolates obtained from clinically apparent infections, were included in the study. Identification of the isolates was performed by MALDI-TOF mass spectrometry. Susceptibility testing and ESBL detection was performed using VITEK® 2, according to EUCAST v4.0 guidelines. Genotypic analysis was performed using Check-MDR CT103 Microarrays. Results Of the total 112 (50.0%) isolates screen positive for ESBLs, 63.4% (71/112) tested positive for ESBL encoding genes by Check-MDR array, which corresponds to 91.8% (67/73) of the total Enterobacteriaceae and 10.3% (4/39) of nonfermenting Gram-negative bacilli. Among the total ESBL gene positive isolates, 95.8% (68/71) carried blaCTX-M genes with CTX-M group 1 type15 being predominant (66/68; 97.1% of CTX-M genes). The blaCTX-M carrying Enterobacteriaceae (n = 64) isolates showed no resistance against imipenem and meropenem and a moderate resistance rate against tigecycline (14.1%), fosfomycin (10.9%) and amikacin (1.6%) suggesting the effectiveness of these antibiotics against most isolates. On the other hand, all the blaCTX-M positive Enterobacteriaceae showed a multidrug resistant (MDR) phenotype with remarkable co-resistances (non-susceptibility rates) to aminoglycosides (92.2%), fluoroquinolones (78.1%) and trimethoprim/sulfamethoxazol (92.2%). Conclusions This study demonstrates a remarkably high prevalence of blaCTX-M genes among ESBL-producing isolates. The high level of resistance to β-lactam and non-β-lactam antibiotics as well as the trend to a MDR profile associated with the blaCTX-M genes are alarming and emphasize the need for routine diagnostic antimicrobial susceptibility testing for appropriate choice of antimicrobial therapy. Electronic supplementary material The online version of this article (10.1186/s12879-018-3436-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ahmed Zeynudin
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Marchioninistr. 17, 81377, Munich, Germany.,Institute of Health Sciences, Jimma University, Jimma, Ethiopia.,Center for International Health (CIH), University of Munich (LMU), 80802, Munich, Germany
| | - Michael Pritsch
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Marchioninistr. 17, 81377, Munich, Germany.,Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), 80802, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, 80802, Munich, Germany
| | - Sören Schubert
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Marchioninistr. 17, 81377, Munich, Germany
| | - Maxim Messerer
- Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Gabriele Liegl
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Marchioninistr. 17, 81377, Munich, Germany
| | - Michael Hoelscher
- Center for International Health (CIH), University of Munich (LMU), 80802, Munich, Germany.,Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), 80802, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, 80802, Munich, Germany
| | - Tefara Belachew
- Institute of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Andreas Wieser
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Marchioninistr. 17, 81377, Munich, Germany. .,Institute of Health Sciences, Jimma University, Jimma, Ethiopia. .,Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), 80802, Munich, Germany. .,German Center for Infection Research (DZIF), Partner Site Munich, 80802, Munich, Germany.
| |
Collapse
|
161
|
Patel MP, Hu L, Brown CA, Sun Z, Adamski CJ, Stojanoski V, Sankaran B, Prasad BVV, Palzkill T. Synergistic effects of functionally distinct substitutions in β-lactamase variants shed light on the evolution of bacterial drug resistance. J Biol Chem 2018; 293:17971-17984. [PMID: 30275013 DOI: 10.1074/jbc.ra118.003792] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/26/2018] [Indexed: 11/06/2022] Open
Abstract
The CTX-M β-lactamases have emerged as the most widespread extended-spectrum β-lactamases (ESBLs) in Gram-negative bacteria. These enzymes rapidly hydrolyze cefotaxime, but not the related cephalosporin, ceftazidime. ESBL variants have evolved, however, that provide enhanced ceftazidime resistance. We show here that a natural variant at a nonactive site, i.e. second-shell residue N106S, enhances enzyme stability but reduces catalytic efficiency for cefotaxime and ceftazidime and decreases resistance levels. However, when the N106S variant was combined with an active-site variant, D240G, that enhances enzyme catalytic efficiency, but decreases stability, the resultant double mutant exhibited higher resistance levels than predicted on the basis of the phenotypes of each variant. We found that this epistasis is due to compensatory effects, whereby increased stability provided by N106S overrides its cost of decreased catalytic activity. X-ray structures of the variant enzymes in complex with cefotaxime revealed conformational changes in the active-site loop spanning residues 103-106 that were caused by the N106S substitution and relieve steric strain to stabilize the enzyme, but also alter contacts with cefotaxime and thereby reduce catalytic activity. We noted that the 103-106 loop conformation in the N106S-containing variants is different from that of WT CTX-M but nearly identical to that of the non-ESBL, TEM-1 β-lactamase, having a serine at the 106 position. Therefore, residue 106 may serve as a "switch" that toggles the conformations of the 103-106 loop. When it is serine, the loop is in the non-ESBL, TEM-like conformation, and when it is asparagine, the loop is in a CTX-M-like, cefotaximase-favorable conformation.
Collapse
Affiliation(s)
- Meha P Patel
- From the Interdepartmental Graduate Program in Translational Biology and Molecular Medicine; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Liya Hu
- Verna Marrs McLean Department of Biochemistry and Molecular Biology
| | - Cameron A Brown
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Zhizeng Sun
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Carolyn J Adamski
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030; Verna Marrs McLean Department of Biochemistry and Molecular Biology
| | - Vlatko Stojanoski
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030; Verna Marrs McLean Department of Biochemistry and Molecular Biology
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | | | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030; Verna Marrs McLean Department of Biochemistry and Molecular Biology.
| |
Collapse
|
162
|
Dagher C, Salloum T, Alousi S, Arabaghian H, Araj GF, Tokajian S. Molecular characterization of Carbapenem resistant Escherichia coli recovered from a tertiary hospital in Lebanon. PLoS One 2018; 13:e0203323. [PMID: 30188911 PMCID: PMC6126819 DOI: 10.1371/journal.pone.0203323] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022] Open
Abstract
The emergence of carbapenem resistant Escherichia coli represents a serious public health concern. This study investigated the resistome, virulence, plasmids content and clonality of 27 carbapenem resistant E. coli isolated from 27 hospitalized patients at the American University of Beirut Medical Center (AUBMC) in Lebanon between 2012 and 2016. Whole-genome sequencing (WGS) data were used to identify resistance determinants. Multilocus sequence typing (MLST), pulsed field gel electrophoresis (PFGE), phylogenetic grouping and PCR-based replicon typing (PBRT) were also performed. The 27 isolates were distributed into 15 STs, of which ST405 (14.8%; n = 4) was the most prevalent. All of the 27 isolates were carbapenem resistant and 20 (74%) were extended-spectrum β-lactamase (ESBL) gene carriers. The predominant detected carbapenemases were blaOXA-48 (48.1%; n = 13) and blaOXA-181 (7.4%; n = 2), for the ESBLs it was blaCTX-M-15 (55.6%; n = 15) and blaCTX-M-24 (18.5%; n = 5), and for the AmpC-type β-lactamases, blaCMY-42 (40.7%; n = 11) and blaCMY-2 (3.7%; n = 1). Thirteen replicons were identified among the 27 E. coli isolates including: IncL/M, IncFIA, IncFIB, IncFII, IncI1, and IncX3. PFGE revealed a high genetic diversity with the 27 isolates being grouped in 21 different pulsotypes. SNPs analysis and PFGE showed a possible clonal dissemination of ST405, ST1284, ST354 and ST410 and the dominance of certain STs, monitoring of which could help in elucidating routes of transmission. This study represents the first WGS-based in depth analysis of the resistomes and mobilomes of carbapenem resistant E. coli in Lebanon.
Collapse
Affiliation(s)
- Christel Dagher
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Sahar Alousi
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Harout Arabaghian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - George F. Araj
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
- * E-mail:
| |
Collapse
|
163
|
Combination of Amino Acid Substitutions Leading to CTX-M-15-Mediated Resistance to the Ceftazidime-Avibactam Combination. Antimicrob Agents Chemother 2018; 62:AAC.00357-18. [PMID: 29941650 DOI: 10.1128/aac.00357-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/20/2018] [Indexed: 01/26/2023] Open
Abstract
Single amino acid substitutions in the Ω loop of KPC β-lactamases are known to lead to resistance to the ceftazidime-avibactam combination. Here, we investigate this mechanism of resistance in CTX-M enzymes, which are the most widely spread extended-spectrum β-lactamases worldwide. Nine single amino acid polymorphisms were identified in the Ω loop of the 172 CTX-M sequences present in the Lahey database of β-lactamases. The corresponding modifications were introduced in CTX-M-15 by site-directed mutagenesis. None of the nine substitutions was associated with ceftazidime-avibactam resistance in Escherichia coli TOP10. However, two substitutions led to 4-fold (P167S) and 16-fold (L169Q) increases in the MIC of ceftazidime. We determined whether these substitutions favor the in vitro selection of mutants resistant to ceftazidime-avibactam. The selection provided mutants for the L169Q substitution but not for the P167S substitution or for the parental enzyme CTX-M-15. Resistance to the drug combination (MIC of ceftazidime, 16 μg/ml in the presence of 4 μg/ml of avibactam) resulted from the acquisition of the S130G substitution by CTX-M-15 L169Q. Purified CTX-M-15 with the two substitutions, L169Q and S130G, was only partially inhibited by avibactam at concentrations as high as 50,000 μM but retained ceftazidime hydrolysis activity with partially compensatory decreases in kcat and Km These results indicate that emergence of resistance to the ceftazidime-avibactam combination requires more than one mutation in most CTX-M-encoding genes. Acquisition of resistance could be restricted to rare variants harboring predisposing polymorphisms such as Q at position 169 detected in a single naturally occurring CTX-M enzyme (CTX-M-93).
Collapse
|
164
|
Tadesse DA, Li C, Mukherjee S, Hsu CH, Bodeis Jones S, Gaines SA, Kabera C, Loneragan GH, Torrence M, Harhay DM, McDermott PF, Zhao S. Whole-Genome Sequence Analysis of CTX-M Containing Escherichia coli Isolates from Retail Meats and Cattle in the United States. Microb Drug Resist 2018; 24:939-948. [PMID: 30148698 PMCID: PMC6154757 DOI: 10.1089/mdr.2018.0206] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In recent years, there have been increased reports on the detection of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Salmonella strains from food-producing animals and animal products in the United States. We characterized 18 ESBL E. coli isolates from cattle (n = 5), chicken breast (n = 5), ground turkey (n = 6), ground beef (n = 1), and pork chops (n = 1) that were collected by the National Antimicrobial Resistance Monitoring System (NARMS) between 2011 and 2015. In vitro antimicrobial susceptibility testing was done against a panel of 14 antimicrobials followed by a secondary panel of 9 β-lactam agents. Whole-genome sequencing was used to characterize the resistome, plasmids, and the genetic structures of the ESBL genes. All ESBL-producing E. coli isolates were resistant to at least three antimicrobial classes and carried various blaCTX-M genes. Most of the cattle and ground turkey isolates carried blaCTX-M-27. In chicken breast isolates, blaCTX-M-1 was present as part of an ISEcp1 transposition unit carried on a plasmid that shares sequence similarity with the backbone structure of the IncI plasmid. Isolates carrying the blaCTX-M-14 and blaCTX-M-15 genes, widely distributed in human clinical isolates, were also isolated. To our knowledge, this is the first report of the widely distributed blaCTX-M-14 and blaCTX-M-15 in E. coli isolates from retail meat samples in the United States. Different insertional sequences were identified upstream of these blaCTX-Ms, including ISEcp1, IS26, and IS903-D. CTX-M in E. coli from food animals and retail chicken breast were often present on plasmids with other resistance genes. Other resistance genes identified included aadA, strA, strB, aac(3)-IId, aac(3)-VIa, aph(3′)-Ic, blaTEM, blaHERA-3, floR, sul1, sul2, catA1, tetA, tetB, dfrA, and qacE. These data describe the emergence of CTX-M-carrying E. coli isolates in food animals and animal products monitored by NARMS program.
Collapse
Affiliation(s)
- Daniel A Tadesse
- 1 Division of Animal and Food Microbiology , U.S. FDA, CVM, Laurel, Maryland
| | - Cong Li
- 1 Division of Animal and Food Microbiology , U.S. FDA, CVM, Laurel, Maryland
| | - Sampa Mukherjee
- 1 Division of Animal and Food Microbiology , U.S. FDA, CVM, Laurel, Maryland
| | - Chih-Hao Hsu
- 1 Division of Animal and Food Microbiology , U.S. FDA, CVM, Laurel, Maryland
| | - Sonya Bodeis Jones
- 1 Division of Animal and Food Microbiology , U.S. FDA, CVM, Laurel, Maryland
| | - Stuart A Gaines
- 1 Division of Animal and Food Microbiology , U.S. FDA, CVM, Laurel, Maryland
| | - Claudine Kabera
- 1 Division of Animal and Food Microbiology , U.S. FDA, CVM, Laurel, Maryland
| | - Guy H Loneragan
- 2 Texas Tech University , Department of Animal and Food Science, Lubbock, Texas
| | - Mary Torrence
- 3 U.S. FDA-CFSAN, Office of Applied Research and Safety Assessment (OARSA) , Laurel, Maryland
| | - Dayna M Harhay
- 4 USDA-ARS, U.S. Meat Animal Research Center, Meat Safety and Quality Research Unit, Clay Center , Nebraska
| | - Patrick F McDermott
- 1 Division of Animal and Food Microbiology , U.S. FDA, CVM, Laurel, Maryland
| | - Shaohua Zhao
- 1 Division of Animal and Food Microbiology , U.S. FDA, CVM, Laurel, Maryland
| |
Collapse
|
165
|
In Vitro Activity of Imipenem-Relebactam and Ceftolozane-Tazobactam against Resistant Gram-Negative Bacilli. Antimicrob Agents Chemother 2018; 62:AAC.00533-18. [PMID: 29760145 DOI: 10.1128/aac.00533-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/07/2018] [Indexed: 11/20/2022] Open
Abstract
Understanding which antimicrobial agents are likely to be active against Gram-negative bacilli can guide selection of antimicrobials for empirical therapy as mechanistic rapid diagnostics are adopted. In this study, we determined the MICs of a novel β-lactam-β-lactamase inhibitor combination, imipenem-relebactam, along with ceftolozane-tazobactam, imipenem, ertapenem, meropenem, ceftriaxone, and cefepime, against 282 drug-resistant isolates of Gram-negative bacilli. For isolates harboring blaKPC (n = 110), the addition of relebactam to imipenem lowered the MIC50/MIC90 from 16/>128 μg/ml for imipenem alone to 0.25/1 μg/ml. For isolates harboring blaCTX-M (n = 48), the MIC50/MIC90 of ceftolozane-tazobactam were 0.5/16 μg/ml (83% susceptible). For isolates harboring blaCMY-2 (n = 17), the MIC50/MIC90 of ceftolozane-tazobactam were 4/8 μg/ml (47% susceptible). Imipenem-relebactam was active against most KPC-producing (but not NDM- or IMP-producing) Enterobacteriaceae and is an encouraging addition to the present antibiotic repertoire.
Collapse
|
166
|
Rapid in vitro detection of CTX-M groups 1, 2, 8, 9 resistance genes by LAMP assays. PLoS One 2018; 13:e0200421. [PMID: 30021007 PMCID: PMC6051616 DOI: 10.1371/journal.pone.0200421] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 06/26/2018] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The prevalence of bacteria producing CTX-M Extended-Spectrum β-lactamases (ESBLs) has increased around the world and some of them became a major cause of infections such as bloodstream or urinary tract infections (UTI). We developed a loop-mediated isothermal amplification (LAMP) assay for a simple, rapid and sensitive detection of the four most common CTX-M groups, namely CTX-M groups 1, 2, 8 and 9. METHODS LAMP primers targeting the four ESBLs CTX-M groups were designed using the Primer Explorer V4 software. The detection limit of the method was tested by serial dilution of reference DNAs. The primer specificity of the LAMP reaction was tested on DNA extracted from six strains producing various group of CTX-M and validated using DNA extracted from CTX-M-resistant clinical isolates (isolated from pus, urine, or blood). Results were compared with those of conventional PCR. RESULTS We were able to detect down to 0.1 pg/ul of DNA using the newly developed LAMP assays whereas the minimal amount detectable for conventional PCR was 50 to 100pg/ul, indicating that the LAMP assay was found to have a detection limit at least 500 to 1000 times lower than the PCR. Additionally, representative genes from the CTX-M groups 1, 2, 8 and 9 were amplified using the designed assay and no cross amplification was observed between the four CTX-M groups, demonstrating the specificity of the LAMP assay. Of the 37 clinical strains tested, the four LAMP assays showed 100% sensitivity and 87%, 97%, 100%, 100% specificity for the CTX-M groups 1, 2, 8 and 9 respectively. CONCLUSION Being sensitive, specific, rapid and standard methods, the LAMP assays developed in this study have a potential to be beneficial tools in molecular epidemiology and surveillance studies of the four prevalent EBSLs CTX-M groups even in low cost laboratory.
Collapse
|
167
|
Diversity Determination of CTX-M1 Producing Klebsiella pneumoniae Using Multilocus Variable-Number Tandem Repeat Analysis, Semnan, Iran. Jundishapur J Microbiol 2018. [DOI: 10.5812/jjm.63131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
168
|
Marando R, Seni J, Mirambo MM, Falgenhauer L, Moremi N, Mushi MF, Kayange N, Manyama F, Imirzalioglu C, Chakraborty T, Mshana SE. Predictors of the extended-spectrum-beta lactamases producing Enterobacteriaceae neonatal sepsis at a tertiary hospital, Tanzania. Int J Med Microbiol 2018; 308:803-811. [PMID: 29980372 PMCID: PMC6171784 DOI: 10.1016/j.ijmm.2018.06.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/25/2018] [Accepted: 06/28/2018] [Indexed: 11/27/2022] Open
Abstract
ESBL-PE sepsis was predicted by admission at ICU and ESBL-PE colonization. Neonates infected with ESBL-PE had significantly high mortality. ESBL-producing Klebsiella pneumoniae (ST45) carrying blaCTX-M-15 were predominant. Whole genome SNP analysis revealed clonal origin in 50% of ESBL-PE paired cases with similar sequence type.
The study was conducted to establish predictors of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) neonatal sepsis and mortality in a tertiary hospital, Tanzania. Between July and December 2016, blood culture was performed in neonates with clinical features of sepsis and neonates/mothers/guardians were screened for ESBL colonization. Selected isolates underwent whole genome sequencing to investigate relatedness. Logistic regression analysis was performed to determine predictors for ESBL-PE associated neonatal sepsis and mortality. Neonatal ESBL-PE sepsis was detected in 32(10.5%) of the 304 neonates investigated. Neonatal ESBL-PE sepsis was independently predicted by admission at the Intensive care Unit and positive mother and neonate ESBL-PE colonization. Deaths occurred in 55(18.1%) of neonates. Neonates infected with ESBL-PE, admitted at ICU, increased age and those transferred from other centres had significantly high mortality rates. Gram-negative bacteria formed the majority (76%) of the isolates, of which 77% were ESBL-PE. Virulent Klebsiella pneumoniae ST45 carrying blaCTX-M-15 were commonly isolated from neonates. Klebsiella pneumoniae (ST45) were the predominant cause of ESBL-PE neonatal sepsis and mortality. Improved infection control and antibiotic stewardship are crucial in controlling the spread of resistant strains. Rapid diagnostic tests to detect ESBL-PE in low-income countries are needed to guide treatment and reduce ESBL-PE-associated mortality.
Collapse
Affiliation(s)
- Rehema Marando
- Department of Pediatrics and Child Health, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Jeremiah Seni
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Mariam M Mirambo
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus-Liebig University, Schubertstrasse 81, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Schubertstrasse 81, 35392, Giessen, Germany
| | - Nyambura Moremi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Martha F Mushi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Neema Kayange
- Department of Pediatrics and Child Health, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Festo Manyama
- Department of Pediatrics and Child Health, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus-Liebig University, Schubertstrasse 81, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Schubertstrasse 81, 35392, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus-Liebig University, Schubertstrasse 81, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Schubertstrasse 81, 35392, Giessen, Germany
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania.
| |
Collapse
|
169
|
Eskandari-Nasab E, Moghadampour M, Tahmasebi A. Prevalence of blaCTX-M Gene among Extended-Spectrum β-Lactamases Producing Klebsiella pneumoniae Clinical Isolates in Iran: A Meta-Analysis. IRANIAN JOURNAL OF MEDICAL SCIENCES 2018; 43:347-354. [PMID: 30046202 PMCID: PMC6055219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND CTX-M-type extended-spectrum β-lactamases (ESBLs) are the most prevalent ESBLs in bacterial members of Enterobacteriaceae family including Klebsiella pneumoniae. The global spread of CTX-M-producing K. pneumoniae is a major concern in most countries including Iran. The aim of this meta-analysis was to determine the relative frequency (RF) of blaCTX-M gene among ESBLs-producing K. pneumoniae clinical isolates in Iran and to report an overall prevalence. METHODS A comprehensive literature search of studies published up to July 2016 was carried out. The keywords "Enterobacteriaceae", "Klebsiella pneumoniae", "ESBLs", "CTX-M" and "Iran" were searched in PubMed, Scopus, EBSCO, Google Scholar, Scirus, SID and IranMedex in both English and Persian. Selected articles were published between July 2010 and July 2016 and all of them were in English. STATA SE version 11.0 was used for statistical analysis. RESULTS Twenty-four articles/abstracts were included in this analysis. Selected studies were performed in Ahvaz, Arak, Ilam, Kashan, Kerman, Mashhad, Shiraz, Tabriz, Tehran, Zabol, and Zahedan. Our pooled evidence showed that the RF of blaCTX-M gene among ESBLs-producing K. pneumoniae clinical isolates varied from 7.7% in Tabriz to 100% in Mashhad, Tehran, and Zahedan, with an overall RF of 56.7%. CONCLUSION Our meta-analysis revealed that the RF of CTX-M-type ESBLs-producing K. pneumoniae is diverse in different regions of Iran, and the central and eastern regions had higher prevalence rates compared to western regions.
Collapse
Affiliation(s)
- Ebrahim Eskandari-Nasab
- Genetic of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mehdi Moghadampour
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Arezoo Tahmasebi
- Department of Statistical and Actuarial Sciences, University of Western Ontario (UWO), London, ON, Canada
| |
Collapse
|
170
|
Diversity of CTX-M-1-producing E. coli from German food samples and genetic diversity of the bla CTX-M-1 region on IncI1 ST3 plasmids. Vet Microbiol 2018; 221:98-104. [PMID: 29981716 DOI: 10.1016/j.vetmic.2018.06.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/07/2018] [Accepted: 06/07/2018] [Indexed: 11/22/2022]
Abstract
Antimicrobial resistance to cephalosporins is commonly mediated by extended-spectrum β-lactamases (ESBL) or plasmidic AmpC β-lactamases (pAmpC). In livestock blaCTX-M-1 is the most frequently detected ESBL-encoding gene. As transmission to consumers through contaminated food is often proposed, this study characterized ESBL/pAmpC-producing E. coli collected from food samples. Therefore, samples from food products of animal origin and vegetables were screened for phenotypically resistant E. coli by selective cultivation. The ESBL genotype was confirmed for 404 isolates with the majority of them (n = 212) harboring the blaCTX-M-1 gene. PFGE and MLST analyses as well as plasmid characterization were carried out for 89 isolates, selected under epidemiological aspects. In addition, 44 isolates were investigated by whole genome sequencing and/or sequencing of their plasmids on an Illumina Miseq platform. MLST and PFGE indicated a diverse population of CTX-M-1-producing E. coli in German food samples with no spread of single clonal lineages. The majority of the isolates harbored the blaCTX-M-1 gene on IncI1 plasmids. Frequently, the gene was associated with the ISEcp1 element and located on a ∼100 kb IncI1 plasmid depicting the plasmid multilocus sequence type (ST) 3. The blaCTX-M-1 gene and its flanking sequences were located within the shufflon of the type IV pilus region in diverse orientations. In conclusion, dissemination of the CTX-M-1 β-lactamase within food samples of animal origin is driven by the transmission of a ∼100 kb large IncI1 ST3 plasmid. Apart from conjugal transfer of IncI1 ST3 plasmids the transmission of the blaCTX-M-1 gene might be further promoted through mobilization due to its location within a recombination hot-spot of IncI1 plasmids.
Collapse
|
171
|
Wyres KL, Holt KE. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr Opin Microbiol 2018; 45:131-139. [PMID: 29723841 DOI: 10.1016/j.mib.2018.04.004] [Citation(s) in RCA: 271] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 04/15/2018] [Indexed: 11/18/2022]
Abstract
Klebsiella pneumoniae is an opportunistic bacterial pathogen known for its high frequency and diversity of antimicrobial resistance (AMR) genes. In addition to being a significant clinical problem in its own right, K. pneumoniae is the species within which several new AMR genes were first discovered before spreading to other pathogens (e.g. carbapenem-resistance genes KPC, OXA-48 and NDM-1). Whilst K. pneumoniae's contribution to the overall AMR crisis is impossible to quantify, current evidence suggests it has a wider ecological distribution, significantly more varied DNA composition, greater AMR gene diversity and a higher plasmid burden than other Gram negative opportunists. Hence we propose it plays a key role in disseminating AMR genes from environmental microbes to clinically important pathogens.
Collapse
Affiliation(s)
- Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia.
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia
| |
Collapse
|
172
|
Müller H, Sib E, Gajdiss M, Klanke U, Lenz-Plet F, Barabasch V, Albert C, Schallenberg A, Timm C, Zacharias N, Schmithausen RM, Engelhart S, Exner M, Parcina M, Schreiber C, Bierbaum G. Dissemination of multi-resistant Gram-negative bacteria into German wastewater and surface waters. FEMS Microbiol Ecol 2018; 94:4963742. [DOI: 10.1093/femsec/fiy057] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/05/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Heike Müller
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Esther Sib
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Mike Gajdiss
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Ursula Klanke
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Franziska Lenz-Plet
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Vanessa Barabasch
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Cathrin Albert
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Anna Schallenberg
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Christian Timm
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Nicole Zacharias
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Ricarda Maria Schmithausen
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Steffen Engelhart
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Martin Exner
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Marijo Parcina
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Christiane Schreiber
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Gabriele Bierbaum
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| |
Collapse
|
173
|
ur Rahman S, Ali T, Ali I, Khan NA, Han B, Gao J. The Growing Genetic and Functional Diversity of Extended Spectrum Beta-Lactamases. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9519718. [PMID: 29780833 PMCID: PMC5892270 DOI: 10.1155/2018/9519718] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/24/2018] [Accepted: 01/31/2018] [Indexed: 11/17/2022]
Abstract
The β-lactams-a large class of diverse compounds-due to their excellent safety profile and broad antimicrobial spectrum are considered to be the most widely used therapeutic class of antibacterials prescribed in human and veterinary clinical practices. This, unfortunately, has also given rise to a continuous increased resistance globally in health care settings as well as in the community due to their permanent selective force driving diversification of the resistance mechanism. Resistance against β-lactams is increasing rapidly as novel β-lactamases, enzymes that degrade β-lactams, are being discovered each day such as recent emergence of extended spectrum β-lactamases (ESBL) that have the ability to inactivate most of the cephalosporins. The complexity and diversity of ESBL are increasing so rapidly that more than 170 variants have thus far been described for only a single genotype, the blaCTX-M -encoding ESBL. This review is to organize all the current updated literature describing genomic features, organization, and mechanism of resistance and mode of dissemination of all known ESBLs.
Collapse
Affiliation(s)
- Sadeeq ur Rahman
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Abdul Wali Khan University, Garden Campus, Khyber Pakhtunkhwa, Pakistan
| | - Tariq Ali
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ijaz Ali
- Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Bioscience Block, Chak Shahzad Campus, Park Road, Islamabad, Pakistan
| | - Nazir Ahmad Khan
- Department of Animal Nutrition, The University of Agriculture, Peshawar, Pakistan
| | - Bo Han
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jian Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
| |
Collapse
|
174
|
Giani T, Antonelli A, Caltagirone M, Mauri C, Nicchi J, Arena F, Nucleo E, Bracco S, Pantosti A, Luzzaro F, Pagani L, Rossolini GM. Evolving beta-lactamase epidemiology in Enterobacteriaceae from Italian nationwide surveillance, October 2013: KPC-carbapenemase spreading among outpatients. ACTA ACUST UNITED AC 2018; 22:30583. [PMID: 28797330 PMCID: PMC5553057 DOI: 10.2807/1560-7917.es.2017.22.31.30583] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 12/20/2016] [Indexed: 12/31/2022]
Abstract
Extended-spectrum beta-lactamases (ESBLs), AmpC-type beta-lactamases (ACBLs) and carbapenemases are among the most important resistance mechanisms in Enterobacteriaceae. This study investigated the presence of these resistance mechanisms in consecutive non-replicate isolates of Escherichia coli (n = 2,352), Klebsiella pneumoniae (n = 697), and Proteus mirabilis (n = 275) from an Italian nationwide cross-sectional survey carried out in October 2013. Overall, 15.3% of isolates were non-susceptible to extended-spectrum cephalosporins but susceptible to carbapenems (ESCR-carbaS), while 4.3% were also non-susceptible to carbapenems (ESCR-carbaR). ESCR-carbaS isolates were contributed by all three species, with higher proportions among isolates from inpatients (20.3%) but remarkable proportions also among those from outpatients (11.1%). Most ESCR-carbaS isolates were ESBL-positive (90.5%), and most of them were contributed by E. coli carrying blaCTX-M group 1 genes. Acquired ACBLs were less common and mostly detected in P. mirabilis. ESCR-carbaR isolates were mostly contributed by K. pneumoniae (25.1% and 7.7% among K. pneumoniae isolates from inpatients and outpatients, respectively), with blaKPC as the most common carbapenemase gene. Results showed an increasing trend for both ESBL and carbapenemase producers in comparison with previous Italian surveys, also among outpatients.
Collapse
Affiliation(s)
- Tommaso Giani
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.,These authors contributed equally to this work
| | - Alberto Antonelli
- These authors contributed equally to this work.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Mariasofia Caltagirone
- Department of Clinical, Surgical, Diagnostic, and Paediatric Sciences, Section of Microbiology, University of Pavia, Pavia, Italy
| | - Carola Mauri
- Microbiology and Virology Unit, Department of Laboratory Medicine, A. Manzoni Hospital, Lecco, Italy
| | - Jessica Nicchi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Fabio Arena
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisabetta Nucleo
- Department of Clinical, Surgical, Diagnostic, and Paediatric Sciences, Section of Microbiology, University of Pavia, Pavia, Italy
| | - Silvia Bracco
- Microbiology and Virology Unit, Department of Laboratory Medicine, A. Manzoni Hospital, Lecco, Italy
| | - Annalisa Pantosti
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Italian National Health Institute, Rome, Italy
| | -
- The AMCLI-CoSA survey participants are listed at the end of the article
| | - Francesco Luzzaro
- Microbiology and Virology Unit, Department of Laboratory Medicine, A. Manzoni Hospital, Lecco, Italy
| | - Laura Pagani
- Department of Clinical, Surgical, Diagnostic, and Paediatric Sciences, Section of Microbiology, University of Pavia, Pavia, Italy
| | - Gian Maria Rossolini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology, Virology and Serology Unit, Florence Careggi University Hospital, Florence, Italy
| |
Collapse
|
175
|
Molecular Epidemiology of Dairy Cattle-Associated Escherichia coli Carrying blaCTX-M Genes in Washington State. Appl Environ Microbiol 2018; 84:AEM.02430-17. [PMID: 29305512 DOI: 10.1128/aem.02430-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/20/2017] [Indexed: 12/31/2022] Open
Abstract
An increase in the prevalence of commensal Escherichia coli carrying blaCTX-M genes among dairy cattle was observed between 2008 and 2012 in Washington State. To study the molecular epidemiology of this change, we selected 126 blaCTX-M-positive and 126 blaCTX-M-negative isolates for determinations of the multilocus sequence types (MLSTs) and antibiotic resistance phenotypes from E. coli obtained during a previous study. For 99 isolates, we also determined the blaCTX-M alleles using PCR and sequencing and identified the replicon types of blaCTX-M-carrying plasmids. The blaCTX-M-negative E. coli isolates comprised 76 sequence types (STs) compared with 32 STs in blaCTX-M-positive E. coli isolates. The blaCTX-M-positive E. coli isolates formed three MLST clonal complexes, accounting for 83% of these isolates; 52% of blaCTX-M-negative E. coli isolates clustered into 10 clonal complexes, and the remainder were singletons. Overall, blaCTX-M-negative E. coli isolates had more diverse genotypes that were distinct to farms, whereas blaCTX-M-positive E. coli isolates had a clonal population structure and were widely disseminated on farms in both regions included in the study. Plasmid replicon types included IncI1 which predominated, followed by IncFIB and IncFIA/FIB. blaCTX-M-15 was the predominant CTX-M gene allele, followed by blaCTX-M-27 and blaCTX-M-14 There was no significant association between plasmid replicon types and bacterial STs, and neither clonal complexes nor major plasmid groups were associated with two discrete dairy-farming regions of Washington State.IMPORTANCE Infections caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli occur globally and present treatment challenges because of their resistance to multiple antimicrobial drugs. Cattle are potential reservoirs of ESBL-producing Enterobacteriaceae, and so understanding the causes of successful dissemination of blaCTX-M genes in commensal bacteria will inform future approaches for the prevention of antibiotic-resistant pathogen emergence.
Collapse
|
176
|
Ding HF, Liu BG, Gao YL, Zhong XH, Duan SS, Yuan L. Divergence of affinities, serotypes and virulence factor between CTX-M Escherichia coli and non-CTX-M producers. Poult Sci 2018; 97:980-985. [PMID: 29272527 DOI: 10.3382/ps/pex376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Indexed: 11/20/2022] Open
Abstract
This study was undertaken to discern the differences of the multi-locus sequence typing (MLST), O serogroups, and virulence factors among 34 CTX-M-1 Escherichia coli, 49 CTX-M-9 strains and 23 non-CTX-M isolates from chickens in Henan province, China. The MLST scheme yielded 34 sequence types, in which ST155 and ST359 were frequent (17% and 15%, respectively) and associated with zoonotic disease. The irp-2 (20% versus 2%, P = 0.0001), traT (85.3% versus 56.5%, P = 0.019), and sfaS (70.6% versus 0, P = 0.021) were significantly more prevalent in CTX-M-1 E. coli than in non-CTX-M producers. Also, CTX-M-9 isolates carried more irp-2 (17% versus 2%, P = 0.023), iroN (71.4% versus 39.1%, P = 0.019), and iss (79.6% versus 39.1%, P = 0.002) genes. In conclusion, although the 106 isolates encompassed a great genetic diversity, the CTX-M isolates harbored more virulence factor genes than non-CTX-M producers.
Collapse
Affiliation(s)
- Hai-Feng Ding
- Henan Agricultural University, Zhengzhou 450002, China
| | - Bao-Guang Liu
- Henan Agricultural University, Zhengzhou 450002, China
| | - Yan-Ling Gao
- Animal Husbandry Bureau of Henan Province, Zhengzhou, 450008, China
| | | | - Sha-Sha Duan
- Henan Agricultural University, Zhengzhou 450002, China
| | - Li Yuan
- Henan Agricultural University, Zhengzhou 450002, China
| |
Collapse
|
177
|
Xu Y, Sun H, Bai X, Fu S, Fan R, Xiong Y. Occurrence of multidrug-resistant and ESBL-producing atypical enteropathogenic Escherichia coli in China. Gut Pathog 2018; 10:8. [PMID: 30038667 PMCID: PMC6054294 DOI: 10.1186/s13099-018-0234-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/19/2018] [Indexed: 01/05/2023] Open
Abstract
Background Atypical enteropathogenic Escherichia coli (aEPEC) is regarded as a globally emerging enteropathogen. aEPECs exhibit various level of resistance to a range of antibiotics, which is increasing alarmingly. The present study investigated the antimicrobial resistance of aEPEC isolates recovered from diarrheal patients, healthy carriers, animals, and raw meats. Results Among 267 aEPEC isolates, 146 (54.7%) were resistant to tetracycline, followed by ampicillin (49.4%), streptomycin (46.1%), and piperacillin (41.2%). Multidrug resistance (MDR) was detected in 128 (47.9%) isolates, and 40 MDR isolates were resistant to ≥ 10 antimicrobial agents. A total of 47 (17.6%) aEPEC isolates were identified as extended-spectrum β-lactamase (ESBL)-producers. The blaCTX-M-14 and blaCTX-M-15 genes were predominant among ESBL-producing isolates. Conclusions This investigation depicted the occurrence of multidrug-resistant and ESBL-producing aEPEC isolates in China. The results suggested that it is necessary to continuously monitor the emergence and spread of MDR aEPEC. Electronic supplementary material The online version of this article (10.1186/s13099-018-0234-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yanmei Xu
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Hui Sun
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Xiangning Bai
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Shanshan Fu
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Ruyue Fan
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Yanwen Xiong
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China.,2Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang China
| |
Collapse
|
178
|
Giufrè M, Accogli M, Ricchizzi E, Barbanti F, Farina C, Fazii P, Mattei R, Sarti M, Barozzi A, Buttazzi R, Cosentino M, Nardone M, Savini V, Spigaglia P, Moro ML, Cerquetti M. Multidrug-resistant infections in long-term care facilities: extended-spectrum β-lactamase-producing Enterobacteriaceae and hypervirulent antibiotic resistant Clostridium difficile. Diagn Microbiol Infect Dis 2018; 91:275-281. [PMID: 29571838 DOI: 10.1016/j.diagmicrobio.2018.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/15/2017] [Accepted: 02/23/2018] [Indexed: 11/30/2022]
Abstract
Infections due to multidrug-resistant (MDR) organisms in long-term care facilities (LTCFs) residents constitute a public health concern. This multicenter study investigated the frequency of ESBL-producing pathogens and MDR Clostridium difficile in clinical specimens from LTCF residents in Italy. During October 2014-March 2015, all urine and diarrheic fecal samples from LTCF residents (≥65 years) with suspected urinary tract infection or C. difficile infection, respectively, received for diagnosis by 4 hospital laboratories located in different cities were analyzed. Antibiotic susceptibility testing, characterization of resistance genes, and molecular typing of pathogens were performed. Of 806 urine cultures collected from 626 residents at 44 different LTCFs, 492 were positive for microbial infection. Of these, 158 were positive for at least an ESBL-producing Enterobacteriaceae species (32.1%), with Escherichia coli as the most frequent ESBL pathogen (23.4%) followed by Klebsiella pneumoniae (4.5%). Furthermore, 4 carbapenemase producers (0.8%) (1 E. coli with VIM-1and 3 K. pneumoniae with KPC-3) were detected. The CTX-M-15 type ESBL predominated in both E. coli (71.3%) and K. pneumoniae (77.3%). Most E. coli isolates (82.6%) belonged to the ST131/H30 clone/subclone. For K. pneumoniae, ST307 and ST15 were frequent (31.8% and 22.7%, respectively), but isolates harboring blaKPC-3 belonged to CC258. Of 136 diarrheic fecal samples collected from 111 residents at 26 different LTCFs, 21 (15.4%) were positive for toxigenic C. difficile; of these, 13 (62%) were MDR (resistant to 3 or more antimicrobial agents of different classes). The predominant C. difficile polymerase chain reaction ribotype was 356/607 (42.9%), followed by 018, 449, and 078 (14% each). Public health efforts are needed to contain the diffusion of CTX-M-producing Enterobacteriaceae and MDR C. difficile in LTCF settings.
Collapse
Affiliation(s)
- Maria Giufrè
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marisa Accogli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Fabrizio Barbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | | | | | - Mario Sarti
- S. Agostino-Estense-Baggiovara Hospital, Modena, Italy
| | | | | | | | | | | | - Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Marina Cerquetti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| |
Collapse
|
179
|
Palzkill T. Structural and Mechanistic Basis for Extended-Spectrum Drug-Resistance Mutations in Altering the Specificity of TEM, CTX-M, and KPC β-lactamases. Front Mol Biosci 2018; 5:16. [PMID: 29527530 PMCID: PMC5829062 DOI: 10.3389/fmolb.2018.00016] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 02/08/2018] [Indexed: 11/13/2022] Open
Abstract
The most common mechanism of resistance to β-lactam antibiotics in Gram-negative bacteria is the production of β-lactamases that hydrolyze the drugs. Class A β-lactamases are serine active-site hydrolases that include the common TEM, CTX-M, and KPC enzymes. The TEM enzymes readily hydrolyze penicillins and older cephalosporins. Oxyimino-cephalosporins, such as cefotaxime and ceftazidime, however, are poor substrates for TEM-1 and were introduced, in part, to circumvent β-lactamase-mediated resistance. Nevertheless, the use of these antibiotics has lead to evolution of numerous variants of TEM with mutations that significantly increase the hydrolysis of the newer cephalosporins. The CTX-M enzymes emerged in the late 1980s and hydrolyze penicillins and older cephalosporins and derive their name from the ability to also hydrolyze cefotaxime. The CTX-M enzymes, however, do not efficiently hydrolyze ceftazidime. Variants of CTX-M enzymes, however, have evolved that exhibit increased hydrolysis of ceftazidime. Finally, the KPC enzyme emerged in the 1990s and is characterized by its broad specificity that includes penicillins, most cephalosporins, and carbapenems. The KPC enzyme, however, does not efficiently hydrolyze ceftazidime. As with the TEM and CTX-M enzymes, variants have recently evolved that extend the spectrum of KPC β-lactamase to include ceftazidime. This review discusses the structural and mechanistic basis for the expanded substrate specificity of each of these enzymes that result from natural mutations that confer oxyimino-cephalosporin resistance. For the TEM enzyme, extended-spectrum mutations act by establishing new interactions with the cephalosporin. These mutations increase the conformational heterogeneity of the active site to create sub-states that better accommodate the larger drugs. The mutations expanding the spectrum of CTX-M enzymes also affect the flexibility and conformation of the active site to accommodate ceftazidime. Although structural data are limited, extended-spectrum mutations in KPC may act by mediating new, direct interactions with substrate and/or altering conformations of the active site. In many cases, mutations that expand the substrate profile of these enzymes simultaneously decrease the thermodynamic stability. This leads to the emergence of additional global suppressor mutations that help correct the stability defects leading to increased protein expression and increased antibiotic resistance.
Collapse
Affiliation(s)
- Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States
| |
Collapse
|
180
|
Pérez-Brocal V, Andremont A, Moya A. Isolation in small populations of Wayampi Amerindians promotes endemicity and homogenisation of their faecal virome, but its distribution is not entirely random. FEMS Microbiol Ecol 2018; 94:4768065. [PMID: 29272453 DOI: 10.1093/femsec/fix184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/19/2017] [Indexed: 11/13/2022] Open
Abstract
The isolated community of the Wayampi Amerindians has been extensively studied for the presence of beta lactamase-producing enterobacteria and their gut microbiota. However, no information about their virome was available. This study tries to establish potential associations between the virome and diverse epidemiological data, through the metagenomic study of the faecal prophages and DNA viruses from 31 samples collected in 2010. Taxonomic assignments, composition, abundance and diversity analyses were obtained to characterise the virome and were compared between groups according to several demographic, environmental and medical data. Prophages outnumbered viruses. Composition and abundance of virome indicated relatively low variability. Diversity within samples showed no significant differences, regardless of the group comparison. Significant differences were observed in the beta diversity among samples according to hospitalisation and gender, but not by extended spectrum β-lactamase carriage, antibiotic intake or possession of pets, although some viruses differed in some cases (e.g. immunodeficiency-associated stool virus associated with antibiotic intake). The faecal virome of adult Wayampi is more homogeneous than that from western populations. Not a single factor analysed can explain alone the observed distribution of the virome, but differences by gender (fewer variability in females than males) may reflect differences in life habits and work.
Collapse
Affiliation(s)
- Vicente Pérez-Brocal
- Genomics and Health Area, Foundation for the Promotion of Biomedical and Sanitary Research (FISABIO), Avenida de Cataluña 21, 46020 Valencia, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), c/ Moforte de Lemos 3-5, 28029. Madrid, Spain
| | - Antoine Andremont
- IAME, UMR 1137, INSERM, Université Paris Diderot, 16 rue Henri Huchard B.P. 416-75870 Paris, France
| | - Andrés Moya
- Genomics and Health Area, Foundation for the Promotion of Biomedical and Sanitary Research (FISABIO), Avenida de Cataluña 21, 46020 Valencia, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), c/ Moforte de Lemos 3-5, 28029. Madrid, Spain.,Integrative Systems Biology Institute (I2Sysbio), University of Valéncia and Spanish Research Council (CSIC),c/ Catedrático José Beltrán 2, 46980 Paterna, Valéncia, Spain
| |
Collapse
|
181
|
Navon-Venezia S, Kondratyeva K, Carattoli A. Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol Rev 2018; 41:252-275. [PMID: 28521338 DOI: 10.1093/femsre/fux013] [Citation(s) in RCA: 641] [Impact Index Per Article: 106.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/28/2017] [Indexed: 01/15/2023] Open
Abstract
Klebsiella pneumoniae is an important multidrug-resistant (MDR) pathogen affecting humans and a major source for hospital infections associated with high morbidity and mortality due to limited treatment options. We summarize the wide resistome of this pathogen, which encompasses plentiful chromosomal and plasmid-encoded antibiotic resistance genes (ARGs). Under antibiotic selective pressure, K. pneumoniae continuously accumulates ARGs, by de novo mutations, and via acquisition of plasmids and transferable genetic elements, leading to extremely drug resistant (XDR) strains harboring a 'super resistome'. In the last two decades, numerous high-risk (HiR) MDR and XDR K. pneumoniae sequence types have emerged showing superior ability to cause multicontinent outbreaks, and continuous global dissemination. The data highlight the complex evolution of MDR and XDR K. pneumoniae, involving transfer and spread of ARGs, and epidemic plasmids in highly disseminating successful clones. With the worldwide catastrophe of antibiotic resistance and the urgent need to identify the main pathogens that pose a threat on the future of infectious diseases, further studies are warranted to determine the epidemic traits and plasmid acquisition in K. pneumoniae. There is a need for future genomic and translational studies to decipher specific targets in HiR clones to design targeted prevention and treatment.
Collapse
Affiliation(s)
- Shiri Navon-Venezia
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Kira Kondratyeva
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Alessandra Carattoli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome 00161, Italy
| |
Collapse
|
182
|
Peker N, Rossen JWA, Deurenberg RH, Langereis PC, Raangs EGC, Kluytmans JA, Friedrich AW, Veenemans J, Sinha B. Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis. Microorganisms 2018; 6:microorganisms6010006. [PMID: 29324655 PMCID: PMC5874620 DOI: 10.3390/microorganisms6010006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/27/2022] Open
Abstract
Outbreak management of extended spectrum β-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods. Retrospectively, ESBL-producing bacteria and resistance genes were detected directly from eSwab medium by an accelerated workflow without prior enrichment cultures by an amplicon-based next-generation sequencing (NGS) method, and culture. A total of 27 (18.1%) samples were positive in either test. Sensitivity for CTX-M detection was 96.3% for the phenotypic method and 85.2% for the NGS method, and the specificity was 100% for both methods, as confirmed by micro-array. This resulted in a positive predictive value (PPV) of 100% for both methods, and a negative predictive value (NPV) of 99.2% and 96.8% for the phenotypic method and the NGS method, respectively. Time to result was four days and 14 h for the phenotypic method and the NGS method, respectively. In conclusion, the sensitivity without enrichment shows promising results for further use of amplicon-based NGS for screening during outbreaks.
Collapse
Affiliation(s)
- Nilay Peker
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands.
| | - John W A Rossen
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands.
| | - Ruud H Deurenberg
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands.
| | - Paula C Langereis
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands.
| | - Erwin G C Raangs
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands.
| | - Jan A Kluytmans
- Laboratory for Microbiology and Infection Control, Amphia Hospital, 4818 CK Breda, The Netherlands.
| | - Alexander W Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands.
| | - Jacobien Veenemans
- Laboratory for Microbiology and Infection Control, Amphia Hospital, 4818 CK Breda, The Netherlands.
| | - Bhanu Sinha
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands.
| |
Collapse
|
183
|
Vila J, Sáez-López E, Johnson JR, Römling U, Dobrindt U, Cantón R, Giske CG, Naas T, Carattoli A, Martínez-Medina M, Bosch J, Retamar P, Rodríguez-Baño J, Baquero F, Soto SM. Escherichia coli: an old friend with new tidings. FEMS Microbiol Rev 2018; 40:437-463. [PMID: 28201713 DOI: 10.1093/femsre/fuw005] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/23/2015] [Accepted: 02/04/2016] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli is one of the most-studied microorganisms worldwide but its characteristics are continually changing. Extraintestinal E. coli infections, such as urinary tract infections and neonatal sepsis, represent a huge public health problem. They are caused mainly by specialized extraintestinal pathogenic E. coli (ExPEC) strains that can innocuously colonize human hosts but can also cause disease upon entering a normally sterile body site. The virulence capability of such strains is determined by a combination of distinctive accessory traits, called virulence factors, in conjunction with their distinctive phylogenetic background. It is conceivable that by developing interventions against the most successful ExPEC lineages or their key virulence/colonization factors the associated burden of disease and health care costs could foreseeably be reduced in the future. On the other hand, one important problem worldwide is the increase of antimicrobial resistance shown by bacteria. As underscored in the last WHO global report, within a wide range of infectious agents including E. coli, antimicrobial resistance has reached an extremely worrisome situation that ‘threatens the achievements of modern medicine’. In the present review, an update of the knowledge about the pathogenicity, antimicrobial resistance and clinical aspects of this ‘old friend’ was presented.
Collapse
Affiliation(s)
- J Vila
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - E Sáez-López
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - J R Johnson
- VA Medical Center, Minneapolis, MN, USA, and University of Minnesota, Minneapolis, MN, USA
| | - U Römling
- Karolinska Institute, Stockholm, Sweden
| | - U Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - R Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - C G Giske
- Karolinska Institute, Stockholm, Sweden
| | - T Naas
- Hôpital de Bicêtre, Université Paris Sud, Le Kremlin-Bicêtre, France
| | - A Carattoli
- Department of infectious, parasitic and immune-mediated diseases, Istituto Superiore di Sanità, Rome, Italy
| | - M Martínez-Medina
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona, Spain
| | - J Bosch
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - P Retamar
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Departamento de Medicina, Universidad de Sevilla, Seville, Spain
| | - J Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Departamento de Medicina, Universidad de Sevilla, Seville, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - F Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - S M Soto
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
184
|
Hessman J, Atterby C, Olsen B, Järhult JD. High Prevalence and Temporal Variation of Extended Spectrum β-Lactamase-Producing Bacteria in Urban Swedish Mallards. Microb Drug Resist 2018; 24:822-829. [PMID: 29304312 DOI: 10.1089/mdr.2017.0263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antibiotic resistant bacteria present a growing global healthcare challenge. Previous research demonstrates that wild birds harbor extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae and may contribute to their dissemination. We aimed to assess prevalence and temporal variation in the detection rate of ESBL-producing bacteria in urban wild birds and to evaluate methods regarding sample handling. Monthly fecal sampling was performed in 2013 at an urban pond in Sweden. ESBL-producing Escherichia coli and Klebsiella pneumoniae were analyzed by polymerase chain reaction targeting blaCTX-M. Subsets of samples were analyzed in multiple replicates and without previous freezing. Pond water samples were screened for 12 antibiotics. Out of 813 fecal samples, 47% grew ESBL-producing E. coli, a higher prevalence than in similar studies. Detection rate varied considerably between months, ranging from 4.2% in May to 84% in July, and was significantly higher during warm months. A majority of isolates harbored CTX-M-15 type ESBL. Detection rates were increased by duplicating samples and by avoiding freezing. No antibiotics were detected in pond water. This study demonstrates high prevalence and a previously undescribed temporal variation in detection rate of ESBL-producing Enterobacteriaceae in wild birds. The distribution of CTX-M genes corresponds well with Swedish human isolates, indicating communication between the genetic pools of ESBLs in humans and wild birds. Urban ponds may serve as important natural reservoirs for antimicrobial resistance.
Collapse
Affiliation(s)
- Jon Hessman
- 1 Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University , Uppsala, Sweden
| | - Clara Atterby
- 1 Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University , Uppsala, Sweden
| | - Björn Olsen
- 2 Section of Infectious Diseases, Department of Medical Sciences, Uppsala University , Uppsala Hospital, Sweden
| | - Josef D Järhult
- 2 Section of Infectious Diseases, Department of Medical Sciences, Uppsala University , Uppsala Hospital, Sweden
| |
Collapse
|
185
|
ESBL-producing Escherichia coli
and Its Rapid Rise among Healthy People. Food Saf (Tokyo) 2017; 5:122-150. [PMID: 32231938 DOI: 10.14252/foodsafetyfscj.2017011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/11/2017] [Indexed: 02/06/2023] Open
Abstract
Since around the 2000s, Escherichia coli (E. coli) resistant to both oxyimino-cephalosporins and fluoroquinolones has remarkably increased worldwide in clinical settings. The kind of E. coli is also identified in patients suffering from community-onset infectious diseases such as urinary tract infections. Moreover, recoveries of multi-drug resistant E. coli from the feces of healthy people have been increasingly documented in recent years, although the actual state remains uncertain. These E. coli isolates usually produce extended-spectrum β-lactamase (ESBL), as well as acquisition of amino acid substitutions in the quinolone-resistance determining regions (QRDRs) of GyrA and/or ParC, together with plasmid-mediated quinolone resistance determinants such as Qnr, AAC(6')-Ib-cr, and QepA. The actual state of ESBL-producing E. coli in hospitalized patients has been carefully investigated in many countries, while that in healthy people still remains uncertain, although high fecal carriage rates of ESBL producers in healthy people have been reported especially in Asian and South American countries. The issues regarding the ESBL producers have become very complicated and chaotic due to rapid increase of both ESBL variants and plasmids mediating ESBL genes, together with the emergence of various "epidemic strains" or "international clones" of E. coli and Klebsiella pneumoniae harboring transferable-plasmids carrying multiple antimicrobial resistance genes. Thus, the current state of ESBL producers outside hospital settings was overviewed together with the relation among those recovered from livestock, foods, pets, environments and wildlife from the viewpoint of molecular epidemiology. This mini review may contribute to better understanding about ESBL producers among people who are not familiar with the antimicrobial resistance (AMR) threatening rising globally.
Collapse
|
186
|
Functional Characterization of CTX-M-14 and CTX-M-15 β-Lactamases by In Vitro DNA Shuffling. Antimicrob Agents Chemother 2017; 61:AAC.00891-17. [PMID: 28971870 DOI: 10.1128/aac.00891-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 09/25/2017] [Indexed: 01/25/2023] Open
Abstract
This work investigated the molecular events driving the evolution of the CTX-M-type β-lactamases by the use of DNA shuffling of fragments of the blaCTX-M-14 and blaCTX-M-15 genes. Analysis of a total of 51 hybrid enzymes showed that enzymatic activity could be maintained in most cases, yet hybrids that were active possessed fewer amino acid substitutions than those that were inactive, suggesting that point mutations in the constructs rather than reshuffling of the fragments of the two target genes would more likely cause disruption of CTX-M activity. For example, the P67L and L261P changes in a CTX-M-14 fragment could completely abolish the activity of the enzyme on all antibiotics tested. Structural analysis showed that L216 was located in the active-site β sheet and might interact with the adjacent hydrophobic residues to stabilize the active-site β sheet and maintain the integrity of the enzyme active site. Likewise, a single amino acid substitution, E64K, was found to exhibit a significant suppressive effect on CTX-M-15 activity. Structural analysis showed that E64 might form a salt bridge with R44, disruption of which might affect CTX-M-15 activity. Further analysis of the structure-function relationship of a range of mutant enzymes confirmed that, as can be expected, unstable enzymes lose their activity and avoid selective events. These findings suggest that the distal pockets could also contribute to the activity of the enzymes and may be regarded as alternative targets for inhibitor development.
Collapse
|
187
|
Musicha P, Feasey NA, Cain AK, Kallonen T, Chaguza C, Peno C, Khonga M, Thompson S, Gray KJ, Mather AE, Heyderman RS, Everett DB, Thomson NR, Msefula CL. Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting. J Antimicrob Chemother 2017; 72:1602-1609. [PMID: 28333330 PMCID: PMC5437524 DOI: 10.1093/jac/dkx058] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/01/2017] [Indexed: 12/24/2022] Open
Abstract
Objectives Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi. Methods Ninety-four E. coli isolates from patients admitted to Queen's Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics. Results Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was bla CTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates]. Conclusions This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.
Collapse
Affiliation(s)
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Amy K Cain
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Teemu Kallonen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Chrispin Chaguza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Margaret Khonga
- Microbiology Unit, Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Sarah Thompson
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Katherine J Gray
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Division of Infection and Immunity, University College London, London, UK
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Microbiology Unit, Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| |
Collapse
|
188
|
Characteristics and genetic diversity of multi-drug resistant extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolated from bovine mastitis. Oncotarget 2017; 8:90144-90163. [PMID: 29163817 PMCID: PMC5685738 DOI: 10.18632/oncotarget.21496] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/23/2017] [Indexed: 11/25/2022] Open
Abstract
A characterization of the drug resistance profiles, identification of PCR-based replicon typing, and multilocus sequence typing (MLST) and analysis of 46 ESBL-producing Escherichia coli from cows with mastitis are described. All multidrug-resistant isolates of various phylogenetic groups (A = 31, B1= 3, B2 = 2, D = 10) were ESBL-producers of genotypes CTX-M-15 (29), CTX-M-55 (4), CTX-M-14 (4), CTX-M-3 (1), CTX-M-1 (1), TEM (22) and SHV (8) that were found on conjugative plasmids of diverse incompatibility groups (primarily IncF). Transconjugation experiments indicated successful (100%) trans-conjugation, which was verified phenotypically and genotypically. A total of 28 sequence types (ST) were identified, with 10% of isolates being ST410, and 9 other ST that were assigned arbitrary numbers, reflecting the degree of diversity. Multilocus sequence analysis revealed two lineages, a dominant and a small lineage. Split-decomposition showed intraspecies recombination clearly contributed in genetic recombination generating genotypic diversity among the isolates, and a lack of interspecies recombination. This coherent analysis on genetic structure of multidrug-resistant pathogenic E. coli population isolated from mastitic-milk weaponized with resistance elements from a large, rapidly developing country will be a helpful contribution for epidemiology and surveillance of drug resistance patterns, and understanding their global diversity.
Collapse
|
189
|
Extended-Spectrum Beta-Lactamase–Producing Enterobacteriaceae –Related Urinary Tract Infection in Kidney Transplant Recipients: Risk Factors, Treatment, and Long-Term Outcome. Transplant Proc 2017; 49:1757-1765. [DOI: 10.1016/j.transproceed.2017.06.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/01/2017] [Indexed: 11/18/2022]
|
190
|
Charfi K, Grami R, Ben Jeddou A, Messaoudi A, Mani Y, Bouallegue O, Boujaafar N, Aouni M, Mammeri H, Mansour W. Extended-spectrum β-lactamases and plasmid-mediated quinolone resistance in enterobacterial clinical isolates from neonates in Tunisia. Microb Pathog 2017. [DOI: 10.1016/j.micpath.2017.06.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
191
|
Tong P, Ji X, Chen L, Liu J, Xu L, Zhu L, Zhou W, Liu G, Wang S, Guo X, Feng S, Sun Y. Metagenome analysis of antibiotic resistance genes in fecal microbiota of chickens. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
192
|
Zhang D, Yin Z, Zhao Y, Feng J, Jiang X, Zhan Z, Wu W, Chen W, Wang J, Li J, Zhou D. p1220-CTXM, a pKP048-related IncFII K plasmid carrying bla CTX-M-14 and qnrB4. Future Microbiol 2017; 12:1035-1043. [PMID: 28799786 DOI: 10.2217/fmb-2017-0026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIM This study aimed to characterize plasmid-mediated antimicrobial resistance in clinical Klebsiella pneumoniae 1220 carrying bla CTX-M-14 and qnrB4. MATERIALS & METHODS Plasmid p1220-CTXM was transformed from the 1220 isolate into Escherichia coli through conjugal transfer and then fully sequenced. Antimicrobial susceptibility was determined by VITEK. RESULTS p1220-CTXM was an IncFIIK plasmid genetically closely related to pKP048 and carried resistance markers including bla CTX-M-14, bla DHA-1, qnrB4, sul1 and qacEΔ1, all of which were harbored in a 35.7-kb multidrug-resistant region. bla CTX-M-14 was located in a truncated ISEcp1-bla CTX-M-14-orf477 transposition unit, and qnrB4 and bla DHA-1 were in a truncated qnrB4-bla DHA-1 region. CONCLUSION This study provided the insight into the co-occurrence of bla CTX-M-14 and qnrB4 and the evolution of pKP048-related IncFIIK plasmids.
Collapse
Affiliation(s)
- Defu Zhang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China.,College of Food Science & Project Engineering, Bohai University, Jinzhou 121013, China
| | - Zhe Yin
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Yuzong Zhao
- College of Food Science & Project Engineering, Bohai University, Jinzhou 121013, China
| | - Jiao Feng
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Zhe Zhan
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Weili Wu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Jianrong Li
- College of Food Science & Project Engineering, Bohai University, Jinzhou 121013, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| |
Collapse
|
193
|
Patel MP, Hu L, Stojanoski V, Sankaran B, Venkataram Prasad BV, Palzkill T. The Drug-Resistant Variant P167S Expands the Substrate Profile of CTX-M β-Lactamases for Oxyimino-Cephalosporin Antibiotics by Enlarging the Active Site upon Acylation. Biochemistry 2017; 56:3443-3453. [PMID: 28613873 PMCID: PMC5645026 DOI: 10.1021/acs.biochem.7b00176] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CTX-M β-lactamases provide resistance against the β-lactam antibiotic, cefotaxime, but not a related antibiotic, ceftazidime. β-Lactamases that carry the P167S substitution, however, provide ceftazidime resistance. In this study, CTX-M-14 was used as a model to study the structural changes caused by the P167S mutation that accelerate ceftazidime turnover. X-ray crystallography was used to determine the structures of the P167S apoenzyme along with the structures of the S70G/P167S, E166A/P167S, and E166A mutant enzymes complexed with ceftazidime as well as the E166A/P167S apoenzyme. The S70G and E166A mutations allow capture of the enzyme-substrate complex and the acylated form of ceftazidime, respectively. The results showed a large conformational change in the Ω-loop of the ceftazidime acyl-enzyme complex of the P167S mutant but not in the enzyme-substrate complex, suggesting the change occurs upon acylation. The change results in a larger active site that prevents steric clash between the aminothiazole ring of ceftazidime and the Asn170 residue in the Ω-loop, allowing accommodation of ceftazidime for hydrolysis. In addition, the conformational change was not observed in the E166A/P167S apoenzyme, suggesting the presence of acylated ceftazidime influences the conformational change. Finally, the E166A acyl-enzyme structure with ceftazidime did not exhibit the altered conformation, indicating the P167S substitution is required for the change. Taken together, the results reveal that the P167S substitution and the presence of acylated ceftazidime both drive the structure toward a conformational change in the Ω-loop and that in CTX-M P167S enzymes found in drug-resistant bacteria this will lead to an increased level of ceftazidime hydrolysis.
Collapse
Affiliation(s)
- Meha P. Patel
- Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX 77030
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030
| | - Liya Hu
- Verna Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Vlatko Stojanoski
- Verna Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - B. V. Venkataram Prasad
- Verna Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Timothy Palzkill
- Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX 77030
- Verna Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030
| |
Collapse
|
194
|
Kresken M, Körber-Irrgang B, Pfeifer Y, Werner G. Activity of temocillin against CTX-M-producing Escherichia coli and Klebsiella pneumoniae from Germany. Int J Antimicrob Agents 2017; 51:159-160. [PMID: 28705669 DOI: 10.1016/j.ijantimicag.2017.06.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 06/24/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Michael Kresken
- Antiinfectives Intelligence GmbH, Rheinbach, Germany; Rheinische Fachhochschule Köln gGmbH, Cologne, Germany.
| | | | - Yvonne Pfeifer
- Robert Koch-Institute, FG13 Nosocomial Pathogens and Antibiotic Resistance, Wernigerode, Germany
| | - Guido Werner
- Robert Koch-Institute, FG13 Nosocomial Pathogens and Antibiotic Resistance, Wernigerode, Germany
| |
Collapse
|
195
|
Alevizakos M, Mylonakis E. Colonization and infection with extended-spectrum beta-lactamase producing Enterobacteriaceae in patients with malignancy. Expert Rev Anti Infect Ther 2017; 15:653-661. [PMID: 28659026 DOI: 10.1080/14787210.2017.1348895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) constitute a global threat and are prevalent in both nosocomial and community settings. These pathogens have been associated with delays in initiation of appropriate antimicrobial therapy and worse clinical outcomes. Patients with solid or hematologic malignancy represent a high-risk population for both colonization and infection with ESBL-PE. Areas covered: A description of the microbiology and epidemiology of the ESBL-PE is presented. Also, we explore studies on ESBL-PE colonization and infection, and examine areas where future research is needed. Expert commentary: ESBL-PE constitute an increasing threat to patients with malignancy. Unfortunately, substantial geographic variations as well as knowledge gaps in certain regions of the world limit our ability to reach conclusions that are valid globally. Furthermore, there is limited evidence regarding the optimal ways to prevent and manage infections caused by ESBL-PE. Research is urgently needed to elucidate these areas and allow the institution of appropriate infection control and antimicrobial stewardship policies and recommendations.
Collapse
Affiliation(s)
- Michail Alevizakos
- a Infectious Diseases Division , Warren Alpert Medical School of Brown University, Rhode Island Hospital , Providence , RI , USA
| | - Eleftherios Mylonakis
- a Infectious Diseases Division , Warren Alpert Medical School of Brown University, Rhode Island Hospital , Providence , RI , USA.,b Medical Science (Medicine, and Molecular Microbiology and Immunology) , Warren Alpert Medical School of Brown University, Rhode Island Hospital , Providence , RI , USA
| |
Collapse
|
196
|
Lee K, Yong D, Jeong SH, Tulgaa K, Docquier JD, Rossolini GM, Chong Y. Genetic and biochemical characterisation of CTX-M-37 extended-spectrum β-lactamase from an Enterobacter cloacae clinical isolate from Mongolia. J Glob Antimicrob Resist 2017; 10:3-7. [PMID: 28587869 DOI: 10.1016/j.jgar.2017.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/06/2017] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVES The aims of this study were to determine the resistance level of a blaCTX-M-37-carrying Enterobacter cloacae isolate from Mongolia, to analyse kinetic parameters of the purified enzyme and to compare the genetic environment of the gene. METHODS Minimum inhibitory concentrations (MICs) were determined using the Clinical and Laboratory Standards Institute (CLSI) agar dilution method. Purified CTX-M-37 enzyme was used to determined kinetic parameters. The genetic environment of the blaCTX-M-37 gene in E. cloacae was compared with a Kluyvera cryocrescens isolate. RESULTS The E. cloacae isolate showed relatively low-level resistance to cefotaxime (MIC=16mg/L) compared with a CTX-M-3-producing strain (MIC=256mg/L), and CTX-M-37 had a lower kcat/Km value for cefotaxime (2.0μM-1s-1) compared with CTX-M-3 (3.5μM-1s-1), possibly due to Asn114Asp substitution. The blaCTX-M-37 gene in the E. cloacae isolate was carried on a conjugative plasmid and was associated with an ISEcp1 element containing the -35 and -10 putative promoter sequences TTGAAA and TACAAT, respectively, unlike in the K. cryocrescens isolate. CONCLUSIONS The CTX-M-37-producing E. cloacae isolate showed relatively low-level resistance to cefotaxime and the purified enzyme had lower kinetic parameters as the result of Asn114Asp substitution. Presence of an ISEcp1 element and putative promoters upstream of the blaCTX-M-37 gene in E. cloacae, but not in the K. cryocrescens isolate, indicated their roles in mobilisation and expression of the gene.
Collapse
Affiliation(s)
- Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Khosbayar Tulgaa
- Department of Molecular Biology and Genetics, Research Center of Antimicrobial Resistance, Health Sciences University of Mongolia, Zorig Str. 4, Ulaanbaatar, Mongolia
| | - Jean-Denis Docquier
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 1, I-53100 Siena, Italy
| | - Gian Maria Rossolini
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 1, I-53100 Siena, Italy
| | - Yunsop Chong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea.
| |
Collapse
|
197
|
Bugrysheva JV, Sue D, Gee JE, Elrod MG, Hoffmaster AR, Randall LB, Chirakul S, Tuanyok A, Schweizer HP, Weigel LM. Antibiotic Resistance Markers in Burkholderia pseudomallei Strain Bp1651 Identified by Genome Sequence Analysis. Antimicrob Agents Chemother 2017; 61:e00010-17. [PMID: 28396541 PMCID: PMC5444168 DOI: 10.1128/aac.00010-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/31/2017] [Indexed: 12/30/2022] Open
Abstract
Burkholderia pseudomallei Bp1651 is resistant to several classes of antibiotics that are usually effective for treatment of melioidosis, including tetracyclines, sulfonamides, and β-lactams such as penicillins (amoxicillin-clavulanic acid), cephalosporins (ceftazidime), and carbapenems (imipenem and meropenem). We sequenced, assembled, and annotated the Bp1651 genome and analyzed the sequence using comparative genomic analyses with susceptible strains, keyword searches of the annotation, publicly available antimicrobial resistance prediction tools, and published reports. More than 100 genes in the Bp1651 sequence were identified as potentially contributing to antimicrobial resistance. Most notably, we identified three previously uncharacterized point mutations in penA, which codes for a class A β-lactamase and was previously implicated in resistance to β-lactam antibiotics. The mutations result in amino acid changes T147A, D240G, and V261I. When individually introduced into select agent-excluded B. pseudomallei strain Bp82, D240G was found to contribute to ceftazidime resistance and T147A contributed to amoxicillin-clavulanic acid and imipenem resistance. This study provides the first evidence that mutations in penA may alter susceptibility to carbapenems in B. pseudomallei Another mutation of interest was a point mutation affecting the dihydrofolate reductase gene folA, which likely explains the trimethoprim resistance of this strain. Bp1651 was susceptible to aminoglycosides likely because of a frameshift in the amrB gene, the transporter subunit of the AmrAB-OprA efflux pump. These findings expand the role of penA to include resistance to carbapenems and may assist in the development of molecular diagnostics that predict antimicrobial resistance and provide guidance for treatment of melioidosis.
Collapse
Affiliation(s)
| | - David Sue
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jay E Gee
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mindy G Elrod
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Linnell B Randall
- Department of Molecular Genetics and Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Sunisa Chirakul
- Department of Molecular Genetics and Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Apichai Tuanyok
- Department of Molecular Genetics and Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Herbert P Schweizer
- Department of Molecular Genetics and Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Linda M Weigel
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| |
Collapse
|
198
|
Giufrè M, Ricchizzi E, Accogli M, Barbanti F, Monaco M, Pimentel de Araujo F, Farina C, Fazii P, Mattei R, Sarti M, Barozzi A, Buttazzi R, Cosentino M, Nardone M, Savini V, Spigaglia P, Pantosti A, Moro ML, Cerquetti M. Colonization by multidrug-resistant organisms in long-term care facilities in Italy: a point-prevalence study. Clin Microbiol Infect 2017; 23:961-967. [PMID: 28412380 DOI: 10.1016/j.cmi.2017.04.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/30/2017] [Accepted: 04/06/2017] [Indexed: 11/24/2022]
Abstract
OBJECTIVES To determine prevalence and risk factors for colonization by multidrug-resistant organisms (MDROs) in long-term care facility (LTCF) residents in Italy. Genotypes of MDRO isolates were investigated. METHODS A point-prevalence study was conducted at 12 LTCFs located in four Italian cities (2 February to 14 March 2015). Rectal swabs, faeces and nasal/auxiliary swabs were cultured for extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacteriaceae, Clostridium difficile and methicillin-resistant Staphylococcus aureus (MRSA) respectively. Antimicrobial susceptibility testing, detection of ESBL and/or carbapenemase genes and molecular typing of MDROs were performed. Risk factors for colonization were determined by univariate and multivariate analysis. RESULTS A total of 489 LTCF residents aged ≥65 years were enrolled. The prevalence of colonization by ESBL-producing Enterobacteriaceae, MRSA and C. difficile was 57.3% (279/487), 17.2% (84/487) and 5.1% (21/409) respectively. Carriage rate of carbapenemase-producing Enterobacteriaceae was 1% (5/487). Being bedridden was a common independent risk factor for colonization by all MDROs, although risk factors specific for each MDRO were identified. ESBL-producing Escherichia coli carriage was associated with the sequence type (ST) 131-H30 subclone, but other minor STs predominated in individual LTCF or in LTCFs located in the same city, suggesting a role for intrafacility or local transmission. Similarly, MRSA from LTCF residents belonged to the same spa types/ST clones (t008/ST8 and t032/ST22) commonly found in Italian acute-care hospitals, but infrequent spa types were recovered in individual LTCFs. The prevalent C. difficile PCR ribotypes were 356/607 and 018, both common in Italian acute-care hospitals. CONCLUSIONS MDRO colonization is common among residents in Italian LTCFs.
Collapse
Affiliation(s)
- M Giufrè
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - E Ricchizzi
- Health and Social Agency, Emilia-Romagna Region, Bologna, Italy
| | - M Accogli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - F Barbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - M Monaco
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - C Farina
- Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - P Fazii
- Spirito Santo Hospital, Pescara, Italy
| | - R Mattei
- Campo di Marte Hospital, Lucca, Italy
| | - M Sarti
- S. Agostino-Estense-Baggiovara Hospital, Modena, Italy
| | - A Barozzi
- S. Agostino-Estense-Baggiovara Hospital, Modena, Italy
| | - R Buttazzi
- Health and Social Agency, Emilia-Romagna Region, Bologna, Italy
| | - M Cosentino
- Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - M Nardone
- Campo di Marte Hospital, Lucca, Italy
| | - V Savini
- Spirito Santo Hospital, Pescara, Italy
| | - P Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - A Pantosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - M L Moro
- Health and Social Agency, Emilia-Romagna Region, Bologna, Italy
| | - M Cerquetti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| |
Collapse
|
199
|
Fleurbaaij F, Goessens W, van Leeuwen HC, Kraakman MEM, Bernards ST, Hensbergen PJ, Kuijper EJ. Direct detection of extended-spectrum beta-lactamases (CTX-M) from blood cultures by LC-MS/MS bottom-up proteomics. Eur J Clin Microbiol Infect Dis 2017; 36:1621-1628. [PMID: 28397101 PMCID: PMC5554287 DOI: 10.1007/s10096-017-2975-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023]
Abstract
Rapid bacterial species identification and antibiotic susceptibility testing in positive blood cultures have an important impact on the antibiotic treatment for patients. To identify extended-spectrum beta-lactamases (ESBL) directly in positive blood culture bottles, we developed a workflow of saponin extraction followed by a bottom-up proteomics approach using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The workflow was applied to positive blood cultures with Escherichia coli and Klebsiella pneumoniae collected prospectively in two academic hospitals over a 4-month period. Of 170 positive blood cultures, 22 (12.9%) contained ESBL-positive isolates based on standard susceptibility testing. Proteomic analysis identified CTX-M ESBLs in 95% of these isolates directly in positive blood cultures, whereas no false positives were found in the non-ESBL producing positive blood cultures. The results were confirmed by molecular characterisation of beta-lactamase genes. Based on this proof-of-concept study, we conclude that LC-MS/MS-based protein analysis can directly identify extended-spectrum beta lactamases in E. coli and K. pneumoniae positive blood cultures, and could be further developed for application in routine diagnostics.
Collapse
Affiliation(s)
- F Fleurbaaij
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - W Goessens
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - H C van Leeuwen
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - M E M Kraakman
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - S T Bernards
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - P J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - E J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands.
| |
Collapse
|
200
|
Biochemical characterization of CTX-M-166, a new CTX-M β-lactamase produced by a commensal Escherichia coli isolate. J Antibiot (Tokyo) 2017; 70:809-810. [PMID: 28377638 DOI: 10.1038/ja.2017.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/20/2017] [Accepted: 02/28/2017] [Indexed: 11/08/2022]
|