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Shropshire WC, Song X, Bremer J, Seo S, Rodriguez S, Anand SS, Dinh AQ, Bhatti MM, Konovalova A, Arias CA, Kalia A, Shamoo Y, Shelburne SA. Comprehensive Assessment of Initial Adaptation of ESBL Positive ST131 Escherichia coli to Carbapenem Exposure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.606066. [PMID: 39211100 PMCID: PMC11360896 DOI: 10.1101/2024.07.31.606066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Background It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in their progression to becoming carbapenem resistant. Methods Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of ST131 C2/ H 30Rx isolate, MB1860, under prolonged, increasing carbapenem exposure was performed using two distinct experimental evolutionary platforms to measure fast vs. slow adaptation. Results All thirteen ESBL positive ST131 strains selected from a diverse (n=184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies with a statistically positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P -value <1e-5). WGS analysis of mutants showed initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in outer membrane porin (Omp) encoding genes in the absence of ESBL gene amplification with subclade specific associations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing bla CTX-M-15 copy numbers via modular, insertion sequence 26 (IS 26 ) mediated pseudocompound transposons (PCTns). Transposase activity driven by PCTn upregulation was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure consistent with clinical observations. Conclusions ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2/ H 30Rx subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.
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Tóth K, Damjanova I, Laczkó L, Buzgó L, Lesinszki V, Ungvári E, Jánvári L, Hanczvikkel A, Tóth Á, Szabó D. Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary. Antibiotics (Basel) 2024; 13:363. [PMID: 38667039 PMCID: PMC11047377 DOI: 10.3390/antibiotics13040363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024] Open
Abstract
Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected for Illumina MiSeq sequencing and 30 isolates for MinION sequencing, followed by hybrid de novo assembly. Five C2/H30Rx and one C1-M27 cluster were identified. C1-M27 isolates harbored the F1:A2:B20 plasmid in 93.9% of cases. Long-read sequencing revealed that blaCTX-M-27 was on plasmids. Among the C2/H30Rx isolates, only six isolates carried the C2-associated F2:A1:B- plasmid type. Of 19 hybrid-assembled C2/H30Rx genomes, the blaCTX-M-15 gene was located on plasmid only in one isolate, while in the other isolates, ISEcp1 or IS26-mediated chromosomal integration of blaCTX-M-15 was detected in unique variations. In one isolate a part of F2:A1:B- plasmid integrated into the chromosome. These results suggest that CTX-M-15-producing C2/H30Rx and CTX-M-27-producing C1-M27 subclades may have emerged and spread in different ways in Hungary. While blaCTX-M-27 was carried mainly on the C1/H30R-associated F1:A2:B20 plasmid, the IncF-like plasmids of C2/H30Rx or its composite transposons have been incorporated into the chromosome through convergent evolutionary processes.
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Affiliation(s)
- Kinga Tóth
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Ivelina Damjanova
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Levente Laczkó
- One Health Institute, Faculty of Health Sciences, University of Debrecen, 4032 Debrecen, Hungary
- HUN-REN-DE Conservation Biology Research Group, University of Debrecen, 4032 Debrecen, Hungary
| | - Lilla Buzgó
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Virág Lesinszki
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Erika Ungvári
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Laura Jánvári
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Adrienn Hanczvikkel
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Ákos Tóth
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Dóra Szabó
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
- HUN-REN-SE Human Microbiota Research Group, 1052 Budapest, Hungary
- Neurosurgical and Neurointervention Clinic, Semmelweis University, 1083 Budapest, Hungary
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Mechesso AF, Na SH, Moon DC, Kim SJ, Choi JH, Song HJ, Yoon SS, Lim SK. Antibiotic Resistance Profiles and Molecular Characteristics of blaCTX-M-15-Carrying Salmonella enterica Serovar Enteritidis Isolates from Healthy and Diseased Chickens in Korea. Foodborne Pathog Dis 2022; 19:663-674. [PMID: 36125409 DOI: 10.1089/fpd.2022.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Salmonella enterica serovar Enteritidis has emerged as a public health concern. The main objectives of this study were therefore to determine the antimicrobial susceptibility profiles of Salmonella Enteritidis and to investigate the molecular characteristics of identified ESBL-producing isolates. In the study, 237 Salmonella Enteritidis isolates (232 isolates from chickens, 4 from cattle, and 1 from a pig) were recovered from carcasses and fecal samples of healthy and diseased food animals between 2010 and 2017. Ceftiofur resistance was noted only in chicken isolates (43%, 102/237), with the highest in healthy chickens and their carcasses (48.3%, 83/172) compared with that in diseased chickens (31.7%, 19/60). All of the ceftiofur-resistant isolates exhibited resistance to multiple antimicrobials. Indeed, a relatively higher percentage of ceftiofur-resistant isolates demonstrated resistance to the tested aminoglycosides and tetracycline compared with the ceftiofur-susceptible strains. In this study, blaCTX-M-15 was the only ESBL gene detected in all of the ceftiofur-resistant isolates. The blaCTX-M-15-carrying isolates belonged to 11 different pulsotypes. The blaCTX-M-15 gene was transferred from 20.6% (21/102) of the blaCTX-M-15-harboring isolates to a recipient Escherichia coli J53. The coexistence of IncHI2/ST2 and IncFIIs/ST1 plasmids was noted in the majority (81.8%, 18/22) of the transconjugants. E. coli J53 transconjugants carrying blaCTX-M-15 gene showed distinct genetic environments, predominantly ISEcp1-blaCTX-M-15-orf477 (15/21, 71.4%). This study demonstrated that healthy chickens and their carcasses act as reservoirs of blaCTX-M-15-carrying Salmonella Enteritidis that can potentially be transmitted to humans.
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Affiliation(s)
- Abraham Fikru Mechesso
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea.,Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Seok-Hyeon Na
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Dong Chan Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Su-Jeong Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Ji-Hyun Choi
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Hyun-Ju Song
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Soon-Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
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Genome Sequence of Carbapenemase-Producing Enterobacter cloacae 0102-4P-1 Harboring the IncC-Type Plasmid with a Multidrug Resistance Site Encoding blaNDM-1, Isolated from Commercially Imported Shrimp. Microbiol Resour Announc 2022; 11:e0105821. [PMID: 35442063 PMCID: PMC9119121 DOI: 10.1128/mra.01058-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A carbapenem-resistant Enterobacter cloacae 0102-4P-1 strain was isolated from commercially imported shrimp in Japan. Here, we present a draft genome sequence. The complete plasmid sequence was also determined by hybrid assembly sequencing using Oxford Nanopore and Illumina methods. The assembled whole genome and plasmid were 5,164,033 bp and 162,852 bp long, respectively.
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Chang MX, Zhang J, Zhang JF, Ding XM, Lu Y, Zhang J, Li R, Jiang HX. Formation, Transmission, and Dynamic Evolution of a Multidrug-Resistant Chromosomally Integrated Plasmid in Salmonella Spp. Front Microbiol 2022; 13:846954. [PMID: 35464949 PMCID: PMC9019673 DOI: 10.3389/fmicb.2022.846954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
IncHI2 plasmids, possessing high flexibility and genetic plasticity, play a vital role in the acquisition and transmission of resistance determinants. Polymorphic mobile genetic elements (MGEs) generated by a chromosomally integrated IncHI2 plasmid in an individual Salmonella isolate have not yet been detected, and the mechanisms of the formation, excision, and dynamic evolution of a multidrug-resistant chromosomally integrated plasmid (MRCP) have remained obscure. Herein, we identified a 260-kb blaCTX–M–55-qnrS1-bearing IncHI2 plasmid within a Salmonella Muenster strain. Plenty of heterogeneous MGEs (new Escherichia coli chromosomally integrated plasmid or circular plasmids with different profiles) were yielded when this MRCP was conjugated into E. coli J53 with a transfer frequency of 10–4–10–5 transconjugants per donor. A bioinformatic analysis indicated that replicative transposition and homologous recombination of IS26 elements were particularly active, and the truncated Tn1721 also played a vital role in the formation of MRCP offspring. More importantly, when released from the chromosome, MRCP could capture and co-transfer adjacent chromosomal segments to form larger plasmid progeny than itself. Stability and growth kinetics assays showed that the biological characteristics of MRCP progeny were differentiated. This study provides an insight into a flexible existence of MRCP. The conversion between vertical and horizontal transmission endowed MRCP with genetic stability as a chromosomal coding structure and transferability as extra-chromosomal elements. This alternation may accelerate the acquisition and persistence of antibiotic resistance of clinical pathogens and enhance their ability to respond to adverse environments, which poses a great challenge to the traditional antibiotic treatment.
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Affiliation(s)
- Man-Xia Chang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jing Zhang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jin-Fei Zhang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao-Min Ding
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yang Lu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jie Zhang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Gomi R, Yamamoto M, Tanaka M, Matsumura Y. Chromosomal integration of blaCTX-M genes in diverse Escherichia coli isolates recovered from river water in Japan. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100144. [PMID: 35909619 PMCID: PMC9325909 DOI: 10.1016/j.crmicr.2022.100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ryota Gomi
- Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, 615-8540, Kyoto, Japan
- Corresponding author
| | - Masaki Yamamoto
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, 606-8507, Kyoto, Japan
| | - Michio Tanaka
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, 606-8507, Kyoto, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, 606-8507, Kyoto, Japan
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Minja CA, Shirima G, Mshana SE. Conjugative Plasmids Disseminating CTX-M-15 among Human, Animals and the Environment in Mwanza Tanzania: A Need to Intensify One Health Approach. Antibiotics (Basel) 2021; 10:antibiotics10070836. [PMID: 34356757 PMCID: PMC8300620 DOI: 10.3390/antibiotics10070836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 11/30/2022] Open
Abstract
Background: Globally, blaCTX-M-15 beta-lactamases are the most popular extended spectrum beta-lactamase alleles that are widely distributed due its mobilisation by mobile genetic elements in several compartments. We aimed to determine the conjugation frequencies and replicon types associated with plasmids carrying blaCTX-M-15 gene from Extended Spectrum Beta-lactamase producing isolates in order to understand the dissemination of resistance genes in different compartments. Material and methods: A total of 51 archived isolates carrying blaCTX-M-15 beta-lactamases were used as donors in this study. Antibiotic susceptibility tests were performed as previously described for both donors and transconjugants. Conjugation experiment was performed by a modified protocol of the plate mating experiment, and plasmid replicon types were screened among donor and transconjugant isolates by multiplex Polymerase Chain Reaction in a set of three primer panels. Results: The conjugation efficiency of plasmids carrying blaCTX-M-15 was 88.2% (45/51) with conjugation frequencies in the order of 10−1 to 10−9 and a 100% transfer efficiency observed among E. coli of animal origin. Majority of donors (n = 21) and transconjugants (n = 14) plasmids were typed as either Inc FIA or Inc FIB. Resistance to non-beta-lactam antibiotics was transferrable in 34/45 (75.6%) of events. Ciprofloxacin, tetracycline and sulphamethoxazole-trimethoprim resistance was co-transferred in 29/34 (85.3%) such events. Gentamicin resistance was transferred in 17/34 (50%) of events. Conclusions: Majority of plasmids carrying blaCTX-M-15 were conjugatively transferred by IncF plasmids along with non-beta lactam resistance. There is a need for more research on plasmids to understand how plasmids especially multi replicon plasmids interact and the effect of such interaction on conjugation. One Health approach is to be intensified to address antimicrobial resistance which is a public health threat.
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Affiliation(s)
- Caroline A. Minja
- School of Life Sciences, Department of Global Health and Biomedical Sciences, Nelson Mandela African Institution of Science and Technology, Arusha 23306, Tanzania;
- Correspondence:
| | - Gabriel Shirima
- School of Life Sciences, Department of Global Health and Biomedical Sciences, Nelson Mandela African Institution of Science and Technology, Arusha 23306, Tanzania;
| | - Stephen E. Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza 33109, Tanzania;
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Yagi N, Hamamoto K, Thi Bui KN, Ueda S, Tawata S, Le DT, Thi Bui MH, Hirai I. A high-throughput sequencing determination method for upstream genetic structure (UGS) of ISEcp1-bla CTX-M transposition unit and application of the UGS to classification of bacterial isolates possessing bla CTX-M. J Infect Chemother 2021; 27:1288-1294. [PMID: 33840596 DOI: 10.1016/j.jiac.2021.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/16/2021] [Accepted: 04/01/2021] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Because blaCTX-M is responsible for resistance of bacteria to the third generation cephalosporins, location of blaCTX-M could be a good indicator for classifying bacterial isolates harboring blaCTX-M in molecular epidemiology. However, determination of blaCTX-M location has been difficult when multiple copies of ISEcp1 were found on bacterial genome. We aimed to establish a high-throughput analytical method for upstream genetic structures (UGS) of ISEcp1 to facilitate determination of blaCTX-M location. METHODS Extracted DNA samples obtained from 168 Escherichia coli isolates possessing blaCTX-M were digested by restriction enzyme, HaeIII, and the digested DNA fragments were ligated with homemade barcode adaptors. Then, DNA fragments containing UGS of ISEcp1 were amplified and subjected to the Nanopore sequencer. RESULTS Nucleotide sequences and locations of 168 UGSs obtained from the examined E. coli isolates were determined. Among the 168 determined UGSs, 150 (89.3%) UGS were confirmed on plasmid and classified into eight types. Interestingly, coding sequence of ISEcp1 transposase gene in seven of the eight types were disrupted by IS26 insertion. The remaining 18 (10.7%) UGSs were observed in identical chromosomal region. The obtained nucleotide sequences the locations of UGSs were confirmed by conventional capillary sequencer and Southern blotting, respectively, and any discrepant result was not observed with these confirmation procedures. CONCLUSIONS Our results indicated that the established method was efficient for simultaneously determining at least 100 different UGS, and suggested that the determined UGSs of ISEcp1-blaCTX-M transposition unit was useful for classification of bacterial isolates harboring blaCTX-M.
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Affiliation(s)
- Nobuyoshi Yagi
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Japan
| | - Kouta Hamamoto
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Japan
| | - Kim Ngan Thi Bui
- Dept. of Food Microbiology and Molecular Biology, National Institute of Nutrition, Viet Nam
| | - Shuhei Ueda
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Japan
| | - Saki Tawata
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Japan
| | - Danh Tuyen Le
- Dept. of Food Microbiology and Molecular Biology, National Institute of Nutrition, Viet Nam
| | - Mai Huong Thi Bui
- Dept. of Food Microbiology and Molecular Biology, National Institute of Nutrition, Viet Nam
| | - Itaru Hirai
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Japan.
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Yasugi M, Hatoya S, Motooka D, Matsumoto Y, Shimamura S, Tani H, Furuya M, Mie K, Miyake M, Nakamura S, Shimada T. Whole-genome analyses of extended-spectrum or AmpC β-lactamase-producing Escherichia coli isolates from companion dogs in Japan. PLoS One 2021; 16:e0246482. [PMID: 33544781 PMCID: PMC7864471 DOI: 10.1371/journal.pone.0246482] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/19/2021] [Indexed: 11/21/2022] Open
Abstract
The emergence and global spread of extended-spectrum or AmpC β-lactamase (ESBL/AmpC)-producing Enterobacteriaceae in companion animals have led to the hypothesis that companion animals might be reservoirs for cross-species transmission because of their close contact with humans. However, current knowledge in this field is limited; therefore, the role of companion animals in cross-species transmission remains to be elucidated. Herein, we studied ESBL/AmpC-producing Enterobacteriaceae, Escherichia coli in particular, isolated from extraintestinal sites and feces of companion dogs. Whole-genome sequencing analysis revealed that (i) extraintestinal E. coli isolates were most closely related to those isolated from feces from the same dog, (ii) chromosomal sequences in the ST131/C1-M27 clade isolated from companion dogs were highly similar to those in the ST131/C1-M27 clade of human origin, (iii) certain plasmids, such as IncFII/pMLST F1:A2:B20/blaCTX-M-27, IncI1/pMLST16/blaCTX-M-15, or IncI1/blaCMY-2 from dog-derived E. coli isolates, shared high homology with those from several human-derived Enterobacteriaceae, (iv) chromosomal blaCTX-M-14 was identified in the ST38 isolate from a companion dog, and (v) eight out of 14 tested ESBL/AmpC-producing E. coli isolates (i.e., ST131, ST68, ST405, and ST998) belonged to the human extraintestinal pathogenic E. coli (ExPEC) group. All of the bla-coding plasmids that were sequenced genome-wide were capable of horizontal transfer. These results suggest that companion dogs can spread ESBL/AmpC-producing ExPEC via their feces. Furthermore, at least some ESBL/AmpC-producing ExPECs and bla-coding plasmids can be transmitted between humans and companion dogs. Thus, companion dogs can act as an important reservoir for ESBL/AmpC-producing E. coli in the community.
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Affiliation(s)
- Mayo Yasugi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Asian Health Science Research Institiute, Osaka Prefecture University, Izumisano, Osaka, Japan
- * E-mail:
| | - Shingo Hatoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Yuki Matsumoto
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shunsuke Shimamura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Hiroyuki Tani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Masaru Furuya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Keiichiro Mie
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Masami Miyake
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Terumasa Shimada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Asian Health Science Research Institiute, Osaka Prefecture University, Izumisano, Osaka, Japan
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Pet and Stray Dogs as Reservoirs of Antimicrobial-Resistant Escherichia coli. Int J Microbiol 2021; 2021:6664557. [PMID: 33564312 PMCID: PMC7850822 DOI: 10.1155/2021/6664557] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/28/2020] [Accepted: 01/14/2021] [Indexed: 11/17/2022] Open
Abstract
The close contact between dogs and humans creates the best bridge for interspecies transmission of antimicrobial-resistant bacteria. The surveillance of its resistance including the detection of extended-spectrum beta-lactamases (ESBLs) in Escherichia coli as indicator bacteria is an important tool to control the use of antimicrobials. The aim of this research was to evaluate the E. coli resistance in strains by phenotypic methods, isolated from pet and stray dogs of La Plata city, Argentina. Faecal samples were collected using rectal swabs from 50 dogs with owners (home dogs = HD) and 50 homeless dogs (stray dogs = SD). They were cultured in 3 MacConkey agar plates, with and without antibiotics (ciprofloxacin and cefotaxime). 197 strains were isolated, of which only 95 strains were biochemically identified as E. coli, 46 strains were from HD, and 49 were from SD. Antimicrobial susceptibility was evaluated by the Kirby-Bauer disk diffusion method. The most prevalent resistance was for tetracycline, streptomycin, and ampicillin. In both groups, the level of resistance to 3rd generation cephalosporins was high, and there were multiresistant strains. There was a higher level of antimicrobial resistance in strains from SD compared to HD. There were 8% of strains suspected of being ESBLs among samples of HD and 36% of SD. One (2%) of the strains isolated from HD and 11 (22%) from SD were phenotypically confirmed as ESBL. Pets and stray dogs are a potential source of E. coli antibiotic resistance in Argentina; therefore, its surveillance must be guaranteed.
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Finton MD, Meisal R, Porcellato D, Brandal LT, Lindstedt BA. Whole Genome Sequencing and Characterization of Multidrug-Resistant (MDR) Bacterial Strains Isolated From a Norwegian University Campus Pond. Front Microbiol 2020; 11:1273. [PMID: 32625184 PMCID: PMC7311804 DOI: 10.3389/fmicb.2020.01273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/19/2020] [Indexed: 11/16/2022] Open
Abstract
The presence of extended-spectrum β-lactamase (ESBL)-producing bacteria in environmental sources has been reported worldwide and constitutes a serious risk of community-acquired infections with limited treatment options. The current study aimed to explore the presence of these worrisome bacteria in a pond located at the Norwegian University of Life Sciences in Ås, Norway. A total of 98 bacterial isolates survived growth on selective chromogenic media and were identified by 16S rRNA Sanger sequencing. All strains were evaluated for the presence of the most commonly found β-lactamases and ESBLs in clinical settings (blaCTX–M groups 1, 2, and 9, blaCMY, blaSHV, and blaTEM) and carbapenemases (blaIMP, blaKPC, blaNDM, blaOXA, blaSFC1, blaVIM) through multiplex PCR. A total of eight strains were determined to contain one or more genes of interest. Phenotypic resistance to 18 antimicrobial agents was assessed and isolates were subjected to whole genome sequencing through a combination of Oxford Nanopore’s MinION and Illumina’s MiSeq. Results revealed the presence of β-lactamase and ESBL-producing Escherichia coli, Klebsiella pneumoniae, Stenotrophomonas maltophilia, and a Paraburkholderia spp. Identified β-lactamases and ESBLs include blaCTX–M, blaTEM, blaCMY, blaSHV and a possible blaKPC-like gene, with both documented and novel sequences established. In addition, two inducible β-lactamases were found, a class A β-lactamase (L1) and a cephalosporinase (L2). All strains were determined to be multidrug resistant and numerous resistance genes to non-β-lactams were observed. In conclusion, this study demonstrates that environmental sources are a potential reservoir of clinically relevant ESBL-producing bacteria that may pose a health risk to humans upon exposure.
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Affiliation(s)
- Misti D Finton
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Roger Meisal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lin T Brandal
- Department of Zoonotic, Food- and Waterborne Infections, Norwegian Institute of Public Health, Oslo, Norway
| | - Bjørn-Arne Lindstedt
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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Rosantia S, Higa T, Yagi N, Tokunaga T, Higa S, Yakabi Y, Shirakawa T, Kuntaman K, Hirai I. Characterization of CTX-M-type-extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae isolated from Indonesian undergraduate medical students of a university in Surabaya, Indonesia. J Infect Chemother 2020; 26:575-581. [DOI: 10.1016/j.jiac.2020.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 01/08/2020] [Accepted: 01/26/2020] [Indexed: 12/30/2022]
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High Prevalence of Colistin-Resistant Escherichia coli with Chromosomally Carried mcr-1 in Healthy Residents in Vietnam. mSphere 2020; 5:5/2/e00117-20. [PMID: 32132160 PMCID: PMC7056805 DOI: 10.1128/msphere.00117-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Elucidation of the mechanism of the wide dissemination of colistin-resistant bacteria in communities of developing countries is an urgent public health issue. In this study, we investigated the genetic background of the colistin resistance gene mcr in E. coli isolates from the fecal microbiota of healthy human residents living in a community in Vietnam with a high prevalence of colistin-resistant E. coli. Our study revealed for the first time, a surprisingly high percentage (36.8%) of colistin-resistant E. coli carrying chromosomal mcr-1, the emergence of which may have occurred recently, in the fecal microbiota of the community residents. The mcr-1 transposon on the chromosome may develop into a more stable genotype by the loss of insertion sequences (ISs). Our results are valuable in understanding the mechanism underlying the increasing prevalence of colistin-resistant bacteria within a community. The wide distribution of colistin-resistant bacteria in developing countries has become a common phenomenon. To understand the mechanisms underlying their distribution, we studied the mcr genetic background of colistin-resistant Escherichia coli isolates from the fecal microbiota of healthy human residents from a community in Vietnam with a high prevalence of colistin-resistant E. coli with mcr. Fifty-seven colistin-resistant isolates were obtained from 98 residents; one isolate was collected from each individual and analyzed for mcr. We found that 36.8% of the isolates carried chromosomal mcr-1. Further, 63.2% and 1.8% of the isolates carried mcr-1 on the plasmid and the plasmid/chromosome, respectively. Whole-genome sequencing of genetically unrelated isolates showed that the majority (6 of 7) of the isolates had the chromosomal mcr-1 in a complete ancestral mcr-1 transposon Tn6330, ISApl1-mcr-1-PAP2-ISApl1, which was inserted at various positions on the chromosomes. In addition, the majority (87.5%) of Tn6330 of mcr-1-carrying plasmids (n = 8) lacked both upstream and downstream ISApl1 transposons. The results obtained in this study indicate that plasmid-to-chromosomal transfer of mcr-1 may have occurred recently in the fecal microbiota of the residents. Additionally, Tn6330 on the chromosome may lose ISApl1 from the transposon during multiplication to gain a more stable mcr-1 state on the chromosome. Stabilization of resistance by the chromosomal incorporation of mcr-1 would be an additional challenge in combating the dissemination of resistant bacteria. IMPORTANCE Elucidation of the mechanism of the wide dissemination of colistin-resistant bacteria in communities of developing countries is an urgent public health issue. In this study, we investigated the genetic background of the colistin resistance gene mcr in E. coli isolates from the fecal microbiota of healthy human residents living in a community in Vietnam with a high prevalence of colistin-resistant E. coli. Our study revealed for the first time, a surprisingly high percentage (36.8%) of colistin-resistant E. coli carrying chromosomal mcr-1, the emergence of which may have occurred recently, in the fecal microbiota of the community residents. The mcr-1 transposon on the chromosome may develop into a more stable genotype by the loss of insertion sequences (ISs). Our results are valuable in understanding the mechanism underlying the increasing prevalence of colistin-resistant bacteria within a community.
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Hamamoto K, Tokunaga T, Yagi N, Hirai I. Characterization of blaCTX-M-14 transposition from plasmid to chromosome in Escherichia coli experimental strain. Int J Med Microbiol 2020; 310:151395. [DOI: 10.1016/j.ijmm.2020.151395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 11/28/2019] [Accepted: 12/29/2019] [Indexed: 11/17/2022] Open
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15
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Environmental Presence and Genetic Characteristics of Carbapenemase-Producing Enterobacteriaceae from Hospital Sewage and River Water in the Philippines. Appl Environ Microbiol 2020; 86:AEM.01906-19. [PMID: 31704681 PMCID: PMC6952235 DOI: 10.1128/aem.01906-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/01/2019] [Indexed: 12/12/2022] Open
Abstract
Carbapenemase-producing Enterobacteriaceae (CPE) cause severe health care-associated infections, and their increasing prevalence is a serious concern. Recently, natural ecosystems have been recognized as important reservoirs of antibiotic resistance genes. We investigated the prevalence and genetic characteristics of CPE isolated from the environment (hospital sewage and river water) in the Philippines and found several CPE, including Escherichia coli and other species, with different carbapenemases. The most prevalent carbapenemase gene type was NDM, which is endemic in clinical settings. This study revealed that isolates belonging to carbapenemase-producing E. coli CC10 and K. pneumoniae sequence type 147 (ST147), which are often detected in clinical settings, were dominant in the natural environment. Our work here provides a report on the presence and characteristics of CPE in the environment in the Philippines and demonstrates that both hospital sewage and river water are contaminated by CPE strains belonging to clinically important clonal groups. This study aimed to evaluate the prevalence and genetic characteristics of carbapenemase-producing Enterobacteriaceae (CPE) in hospital sewage and river water in the Philippines, which has a typical tropical maritime climate. We collected 83 water samples from 7 hospital sewage and 10 river water sites. CPE were identified using CHROMagar mSuperCARBA, and Gram-negative strains were identified using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) or 16S rRNA gene sequencing. Resistance genes in Enterobacteriaceae strains were identified using PCR and DNA sequencing, and transferability of carbapenemase genes from the CPE was investigated with conjugation experiments. Genotyping was performed using multilocus sequence typing (MLST) for Escherichia coli and Klebsiella pneumoniae. Out of 124 Enterobacteriaceae isolates, we identified 51 strains as CPE and divided these into 7 species, 11 E. coli, 14 Klebsiella spp., 15 Enterobacter spp., and 11 others, including 4 additional species. Conjugation experiments via broth mating and using E. coli J53 revealed that 24 isolates can transfer carbapenemase-encoding plasmids. MLST analysis showed that 6 of 11 E. coli isolates belonged to clonal complex 10 (CC10). Of 11 K. pneumoniae strains, 9 unique sequence types (STs) were identified, including ST147. Five types of carbapenemase genes were identified, with the most prevalent being NDM (n = 39), which is epidemic in clinical settings in the Philippines. E. coli CC10 and K. pneumoniae ST147, which are often detected in clinical settings, were the dominant strains. In summary, our results indicate that hospital sewage and river water are contaminated by CPE strains belonging to clinically important clonal groups. IMPORTANCE Carbapenemase-producing Enterobacteriaceae (CPE) cause severe health care-associated infections, and their increasing prevalence is a serious concern. Recently, natural ecosystems have been recognized as important reservoirs of antibiotic resistance genes. We investigated the prevalence and genetic characteristics of CPE isolated from the environment (hospital sewage and river water) in the Philippines and found several CPE, including Escherichia coli and other species, with different carbapenemases. The most prevalent carbapenemase gene type was NDM, which is endemic in clinical settings. This study revealed that isolates belonging to carbapenemase-producing E. coli CC10 and K. pneumoniae sequence type 147 (ST147), which are often detected in clinical settings, were dominant in the natural environment. Our work here provides a report on the presence and characteristics of CPE in the environment in the Philippines and demonstrates that both hospital sewage and river water are contaminated by CPE strains belonging to clinically important clonal groups.
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Tanaka H, Hayashi W, Iimura M, Taniguchi Y, Soga E, Matsuo N, Kawamura K, Arakawa Y, Nagano Y, Nagano N. Wastewater as a Probable Environmental Reservoir of Extended-Spectrum-β-Lactamase Genes: Detection of Chimeric β-Lactamases CTX-M-64 and CTX-M-123. Appl Environ Microbiol 2019; 85:e01740-19. [PMID: 31519655 PMCID: PMC6821968 DOI: 10.1128/aem.01740-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/06/2019] [Indexed: 02/06/2023] Open
Abstract
The presence of antimicrobial-resistant bacteria and resistance genes in aquatic environments is a serious public health concern. This study focused on Escherichia coli possessing blaCTX-M genes in wastewater inflows. Twelve crude inflow water samples from wastewater treatment plant (WWTP) A and two samples each from three other WWTPs were collected in 2017 and 2018. A total of 73 E. coli isolates with 31 different sequence types (STs) harboring distinctive blaCTX-M gene repertoires were detected. In WWTP A influents, blaCTX-M-14 (14 isolates) was dominant, followed by blaCTX-M-15 (12 isolates) and blaCTX-M-27 (10 isolates). The chimeric blaCTX-M-64 and blaCTX-M-123 genes were each identified in one of the E. coli isolates from the same WWTP A inflow port. The blaCTX-M-27 gene was associated with five of seven B2-ST131 isolates, including three isolates of the B2-O25b-ST131-H30R/non-Rx lineage. One of the remaining two isolates belonged to the B2-O25b-ST131-H30R/Rx lineage harboring the blaCTX-M-15 gene. As for the B2-O25b-ST131-H30R/non-Rx lineage, two isolates with blaCTX-M-27 were recovered from each of the WWTP B and D influents, and one isolate with blaCTX-M-174 was also recovered from WWTP B influent. Whole-genome sequencing of chimeric blaCTX-M-harboring E. coli isolates revealed that the blaCTX-M-64 gene was integrated into the chromosome of ST10 E. coli B22 via ISEcp1-mediated transposition of a 9,467-bp sequence. The blaCTX-M-123-carrying IncI1 plasmid pB64 was 109,169 bp in length with pST108. The overall findings suggest that wastewater may act as a probable reservoir of clinically significant clonal lineages mediating antimicrobial resistance genes and chimeric genes that have not yet been identified from human isolates of domestic origin in Japan.IMPORTANCE Global spread of CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is a critical concern in both clinical and community settings. This dominance of CTX-M-type ESBL producers may be largely due to the successful international spread of epidemic clones, as represented by the extraintestinal pathogenic Escherichia coli (ExPEC) ST131. Our findings highlight the worrisome presence of diverse E. coli clones associated with humans, including ExPEC lineages harboring the most common blaCTX-M variants in untreated wastewater samples. Moreover, the chimeric genes blaCTX-M-64 and blaCTX-M-123, which have not yet been identified from human isolates of domestic origin in Japan, were identified. Exposure to untreated wastewater through combined sewer overflow caused by heavy rains derived from abnormal weather change could pose a risk for human health due to ingesting those antimicrobial-resistant bacteria.
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Affiliation(s)
- Hayato Tanaka
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Matsumoto, Nagano, Japan
| | - Wataru Hayashi
- Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Matsumoto, Nagano, Japan
| | - Masaki Iimura
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Matsumoto, Nagano, Japan
| | - Yui Taniguchi
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Matsumoto, Nagano, Japan
| | - Eiji Soga
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Matsumoto, Nagano, Japan
| | - Nao Matsuo
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kumiko Kawamura
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yukiko Nagano
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Noriyuki Nagano
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Matsumoto, Nagano, Japan
- Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Matsumoto, Nagano, Japan
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17
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Abstract
While the description of resistance to quinolones is almost as old as these antimicrobial agents themselves, transferable mechanisms of quinolone resistance (TMQR) remained absent from the scenario for more than 36 years, appearing first as sporadic events and afterward as epidemics. In 1998, the first TMQR was soundly described, that is, QnrA. The presence of QnrA was almost anecdotal for years, but in the middle of the first decade of the 21st century, there was an explosion of TMQR descriptions, which definitively changed the epidemiology of quinolone resistance. Currently, 3 different clinically relevant mechanisms of quinolone resistance are encoded within mobile elements: (i) target protection, which is mediated by 7 different families of Qnr (QnrA, QnrB, QnrC, QnrD, QnrE, QnrS, and QnrVC), which overall account for more than 100 recognized alleles; (ii) antibiotic efflux, which is mediated by 2 main transferable efflux pumps (QepA and OqxAB), which together account for more than 30 alleles, and a series of other efflux pumps (e.g., QacBIII), which at present have been sporadically described; and (iii) antibiotic modification, which is mediated by the enzymes AAC(6')Ib-cr, from which different alleles have been claimed, as well as CrpP, a newly described phosphorylase.
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18
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Zhang CZ, Ding XM, Lin XL, Sun RY, Lu YW, Cai RM, Webber MA, Ding HZ, Jiang HX. The Emergence of Chromosomally Located bla CTX-M-55 in Salmonella From Foodborne Animals in China. Front Microbiol 2019; 10:1268. [PMID: 31231347 PMCID: PMC6560199 DOI: 10.3389/fmicb.2019.01268] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/22/2019] [Indexed: 12/02/2022] Open
Abstract
The emergence and increase in prevalence of resistance to cephalosporins amongst isolates of Salmonella from food animals imposes a public health threat. The aim of the present study was to investigate the prevalence and characteristics of CTX-M-producing Salmonella isolates from raw meat and food animals. 27 of 152 (17.76%) Salmonella isolates were ESBL-positive including 21/70 (30%) from food animals and 6/82 (7.32%) from raw meat. CTX-M-55 was the most prevalent ESBL type observed (12/27, 44.44%). 7 of 12 CTX-M-55-positive Salmonella isolates were Salmonella Indiana, 2 were Salmonella Typhimurium, 2 were Salmonella Chester, and the remaining isolate was not typeable. Eight CTX-M-55-positive Salmonella isolates were highly resistant to fluoroquinolones (MICCIP = 64 ug/mL) and co-harbored aac(6’)-Ib-cr and oqxAB. Most of the CTX-M-55 positive isolates (11/12) carried blaCTX-M-55 genes on the chromosome, with the remaining isolate carrying this gene on a transferable 280 kb IncHI2 plasmid. A chromosomal blaCTX-M-55 gene from one isolate transferred onto a 250 kb IncHI2 plasmid which was subsequently conjugated into recipient strain J53. PFGE and MLST profiles showed a wide range of strain types were carrying blaCTX-M-55. Our study demonstrates the emergence and prevalence of foodborne Salmonella harboring a chromosomally located blaCTX-M-55 in China. The co-existence of PMQR genes with blaCTX-M-55 in Salmonella isolates suggests co-selection and dissemination of resistance to both fluoroquinolones and cephalosporins in Salmonella via the food chain in China represents a public health concern.
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Affiliation(s)
- Chuan-Zhen Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao-Min Ding
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao-Ling Lin
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ruan-Yang Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yue-Wei Lu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Run-Mao Cai
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Huan-Zhong Ding
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hong-Xia Jiang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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19
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Most Domestic Livestock Possess Colistin-Resistant Commensal Escherichia coli Harboring mcr in a Rural Community in Vietnam. Antimicrob Agents Chemother 2019; 63:AAC.00594-19. [PMID: 30988145 DOI: 10.1128/aac.00594-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Penha Filho RAC, Ferreira JC, Kanashiro AMI, Berchieri Junior A, Darini ALDC. Emergent multidrug-resistant nontyphoidal Salmonella serovars isolated from poultry in Brazil coharboring bla CTX-M-2 and qnrB or bla CMY-2 in large plasmids. Diagn Microbiol Infect Dis 2019; 95:93-98. [PMID: 31221507 DOI: 10.1016/j.diagmicrobio.2019.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/01/2019] [Accepted: 04/04/2019] [Indexed: 02/08/2023]
Abstract
The number of foodborne gastroenteritis caused by nontyphoidal Salmonella (NTS) worldwide is estimated to be 80.3 million each year. Currently, antimicrobial-resistant NTS disseminated in the animal environment increases the risk of aggravated foodborne outbreaks. Poultry are important source of foodborne NTS infections. This study was conducted to evaluate the phenotypic and genotypic characteristics of 83 NTS isolates from poultry, classified within 36 different serovars. The most prevalent serovar was S. Schwarzengrund (10/83), from which 8/10 were multidrug resistant (MDR). The antimicrobial susceptibility testing showed a total of 18 MDR isolates, from which 8/18 coharbored blaCTX-M-2 and qnrB5. The genes qnrB5, blaCTX-M-2, qnrB2, or blaCMY-2 were also found alone in other MDR isolates. All resistance genes were harbored in large plasmids, ranging from 30 to 270 kb. The pColE replicon was present in 8 MDR isolates; however it was not associated with resistance. ISCR1 and class I integron structures were always associated with blaCTX-M-2.
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Affiliation(s)
| | - Joseane Cristina Ferreira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil, 14040-903
| | | | - Angelo Berchieri Junior
- School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil, 14884-900
| | - Ana Lúcia da Costa Darini
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil, 14040-903
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Hamamoto K, Hirai I. Characterisation of chromosomally-located bla CTX-M and its surrounding sequence in CTX-M-type extended-spectrum β-lactamase-producing Escherichia coli isolates. J Glob Antimicrob Resist 2018; 17:53-57. [PMID: 30445208 DOI: 10.1016/j.jgar.2018.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Although it has been regarded that the CTX-M-type extended-spectrum β-lactamase (ESBL) gene blaCTX-M is mainly carried by antimicrobial resistance plasmids, Escherichia coli possessing chromosomally-located blaCTX-M has been reported in previous studies. This study aimed to characterise the genetic structure of the chromosomally-located blaCTX-M transposition unit and its surrounding sequence in ESBL-producing E. coli isolated in a Japanese hospital. METHODS A total of 81 ESBL-producing E. coli isolates were studied. The existence of chromosomally-located blaCTX-M was confirmed by S1 nuclease-digested pulsed-field gel electrophoresis (PFGE) and Southern blot hybridisation and by sequencing analysis of the PCR-amplified DNA fragments. RESULTS Chromosomally-located blaCTX-M was confirmed in 22 (27.2%) of the 81 E. coli isolates examined; five and four location types of chromosomally-located blaCTX-M-14 and blaCTX-M-15 were determined, respectively. Among the 22 E. coli isolates, 15 (68.2%) possessed single chromosomally-located blaCTX-M gene, probably due to single transposition of a plasmidic blaCTX-M to the chromosome. In isolate N0057, the blaCTX-M-15 transposition unit was transferred from a plasmid into two different chromosomal regions. In addition, 'recurrent' transposition of already existing chromosomally-located blaCTX-M-14 to another chromosomal region was observed in isolates N0211, N0214, N01127, N1682 and N1753; consequently, these isolates possessed two copies of chromosomally-located blaCTX-M-14. CONCLUSION Considering that isolates N0211, N0214, N01127, N1682 and N1753 in which the 'recurrent' transposition event occurred were genetically related according to PFGE, these data suggest the possibility of accumulation of blaCTX-M on the chromosome in CTX-M-type ESBL-producing E. coli.
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Affiliation(s)
- Kouta Hamamoto
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan; Japan Society for the Promotion of Science (JSPS), Japan
| | - Itaru Hirai
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan; Japan Agency for Medical Research and Development (AMED)/Japan International Cooperation Agency (JICA), Science and Technology Research Partnership for Sustainable Development (SATREPS), Japan.
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22
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Higa S, Sarassari R, Hamamoto K, Yakabi Y, Higa K, Koja Y, Hirai I. Characterization of CTX-M type ESBL-producing Enterobacteriaceae isolated from asymptomatic healthy individuals who live in a community of the Okinawa prefecture, Japan. J Infect Chemother 2018; 25:314-317. [PMID: 30292768 DOI: 10.1016/j.jiac.2018.09.005] [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: 06/26/2018] [Revised: 08/22/2018] [Accepted: 09/10/2018] [Indexed: 11/25/2022]
Abstract
This study was performed to characterize CTX-M type extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae carriage in asymptomatic health individuals, which has not been well investigated, in a community of the Okinawa prefecture, Japan. Fecal samples were voluntary collected from asymptomatic healthy individuals who were going to take a routine medical checkup. The collected fecal samples were inoculated on MacConkey agar supplemented with 2 μg/ml of cefotaxime and incubated at 37 °C. Randomly selected three lactose-fermented colonies per each sample were analyzed. Genetic relatedness among the CTX-M type ESBL-producing Enterobacteriaceae isolates were performed by pulsed-field gel electrophoresis (PFGE) after confirmation of ESBL phenotype and determination of bacterial species. Location of blaCTX-M was confirmed by S1-PFGE, I-CeuI-PFGE and the Southern blotting hybridization. ESBL-producing Enterobacteriaceae was isolated from 32 (12.2%) of the collected 263 fecal samples, and 96 ESBL-producing Enterobacteriaceae isolates were obtained. CTX-M type ESBL-producing Escherichia coli B2 were major (67 isolates, 72.0%) and 40 (59.7%) of the 67 CTX-M type ESBL -producing E. coli B2 were E. coli B2-ST131. Three CTX-M type ESBL-producing E. coli B2-ST131 isolates from asymptomatic healthy individuals showed similar PFGE band patterns as five CTX-M type ESBL -producing E. coli B2-ST131 isolates from a hospital locates in the same area of the target community. Chromosomally-transferred blaCTX-M was observed in 10.0% of the examined CTX-M type ESBL-producing Enterobacteriaceae isolates. We report current situation CTX-M type ESBL-producing Enterobacteriaceae carriage in asymptomatic healthy individuals of the Okinawa prefecture, Japan. In addition, our results indicated that worldwide distributed CTX-M type ESBL-producing E. coli B2-ST131 has been spread in a community. Therefore monitoring of ESBL-producing Enterobacteriaceae in healthy individuals is important.
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Affiliation(s)
- Seina Higa
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan
| | - Rosantia Sarassari
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan
| | - Kouta Hamamoto
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan
| | - Yasuaki Yakabi
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan
| | - Kanta Higa
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan
| | - Yasuko Koja
- Department of Adult and Gerontological Nursing, Field of Home Care and Chronic Care Nursing, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan
| | - Itaru Hirai
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan.
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23
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ESBL-plasmid carriage in E. coli enhances in vitro bacterial competition fitness and serum resistance in some strains of pandemic sequence types without overall fitness cost. Gut Pathog 2018; 10:24. [PMID: 29983750 PMCID: PMC6003029 DOI: 10.1186/s13099-018-0243-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/13/2018] [Indexed: 12/26/2022] Open
Abstract
Background Extended spectrum beta lactamase (ESBL)-producing extraintestinal pathogenic Escherichia coli infections are of global interest because of their clinical and economic impact. The ESBL resistance genes disseminate through plasmids, and are found in successful global lineages such as ST131 and ST648. The carriage of plasmids has been suggested to result in a fitness burden, but recently it was shown that ESBL-plasmids enhanced virulence in pandemic ST131 and ST648 lineages without affecting their fitness. Herein, we investigated the influence of ESBL-plasmids on bacterial competition and serum resistance, both of which are essential characteristics of ExPEC during infections. Methods Triplets of ESBL-plasmid-carrying wildtype (WT), plasmid-cured variant (PCV) and transformant (T) of five ExPEC strains of ST131 and ST648 were used for bacterial competition experiments with colicin-producing commensal E. coli, competitive adhesion experiments and serum survival. In addition, resilience after SDS, acid, osmotic challenges and RNA sequence data were analyzed. Results In all five strains tested, ESBL-plasmid carriage did not negatively influence E. coli fitness in direct bacterial competition with commensal E. coli in vitro. That is, WTs did not show any disadvantages when compared to their isogenic plasmid-free PCV. For one strain we even found the opposite as PCV17433 was out-competed by a commensal strain, which suggests an even protective role of the ESBL-plasmid carried by the WT17433. Similarly, in the serum-resistance experiments, the PCVs of two strains (PCV17433 and PCV17887) were more sensitive to serum, unlike WTs and Ts. The observed inter-strain differences could be explained by the different genetic content of plasmids carried in those strains. Conclusions Overall, we found no compelling evidence for an increased burden resulting from the carriage of ESBL-plasmids in the absence of antimicrobial selection pressure in the strains of pandemic ST131 and ST648; rather, the possession of certain ESBL-plasmids was beneficial for some strains in regarding competition fitness and serum survival. Electronic supplementary material The online version of this article (10.1186/s13099-018-0243-z) contains supplementary material, which is available to authorized users.
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24
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Ozaki H, Matsuoka Y, Nakagawa E, Murase T. Characteristics of Escherichia coli isolated from broiler chickens with colibacillosis in commercial farms from a common hatchery. Poult Sci 2018. [PMID: 28637225 DOI: 10.3382/ps/pex167] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To investigate the epidemiologic aspects of colibacillosis in broiler chickens, 83 Escherichia coli isolates obtained from the pericarditis and perihepatitis lesions in broiler chickens from 4 commercial farms, 5 isolates recovered from 5 samples of yolk sac contents that were pooled from 25 emaciated chicks, and 4 fecal isolates obtained from a hatchery that supplied chicks to the 4 commercial farms mentioned above were genetically and bacteriologically characterized. Using pulsed-field gel electrophoresis (PFGE), a total of 92 isolates were classified into 33 pulsotypes. Identical pulsotypes were observed in isolates obtained from hatchery samples and the affected broiler chickens on multiple farms at various sampling times. Seventeen representative isolates with no common origin belonging to 6 pulsotypes and an additional 27 isolates with the other pulsotypes were used for further experiments. Isolates with identical pulsotypes exhibited common traits for virulence-associated genes, lipopolysaccharide core types, and phylogenetic groups. Nine of the isolates were serologically typed as O125 with various types of H antigens and 3 were typed as O25:H4. In the 27 isolates resistant to ceftiofur (CTF), which is a third generation cephalosporin, the blaCTX-M-2, blaCMY-2, blaCTX-M-14, blaCTX-M-65 genes were found in 15, 8, 3, and 1 isolate(s), respectively, and another isolate resistant to CTF had both the blaCTX-M-2 and the blaCMY-2 genes. In the 16 isolates with the blaCTX-M-2 gene, the chromosomal location of the gene was identified in 12 isolates. The plasmid-mediated quinolone resistance genes, oqxAB and aac(6')-Ib-cr, were found in 2 and 3 isolates, respectively. Conjugation experiments revealed that the blaCTX-M-2 (4 isolates), blaCTX-M-14 (3 isolates), blaSHV-12 (1 isolate), and oqxAB (2 isolates) genes were transferred. Our data suggest that E. coli strains with identical pulsotypes had been caused the incidences of colibacillosis and that the antimicrobial resistance genes on conjugative plasmids and those integrated into the chromosome may be spread among avian pathogenic E. coli strains in multiple farms.
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Affiliation(s)
- H Ozaki
- Laboratory of Veterinary Microbiology, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan.,The Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - Y Matsuoka
- Laboratory of Veterinary Microbiology, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - E Nakagawa
- Laboratory of Veterinary Microbiology, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - T Murase
- Laboratory of Veterinary Microbiology, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan.,The Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
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25
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Nakayama T, Kumeda Y, Kawahara R, Yamaguchi T, Yamamoto Y. Carriage of colistin-resistant, extended-spectrum β-lactamase-producing Escherichia coli harboring the mcr-1 resistance gene after short-term international travel to Vietnam. Infect Drug Resist 2018; 11:391-395. [PMID: 29559800 PMCID: PMC5856025 DOI: 10.2147/idr.s153178] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Background Due to increasing colistin usage, the dissemination of the colistin-resistant gene mcr-1 has been increasingly investigated. The aim of this study was to determine whether a traveler on a short-term international trip to a developing country could bring mcr-1 back to their home country. Materials and methods Thirty-four travel events from Japan to Vietnam encompassing 19 travelers were assessed. A fecal specimen was collected from each traveler before and after each travel event and was inoculated on CHROMagar containing cefotaxime (CTX). Three to seven colonies exhibiting the characteristics of Escherichia coli were collected. Susceptibility to antibiotics and extended-spectrum β-lactamase (ESBL) production were determined by the disk diffusion method and the double-disk synergy test, respectively. ESBL-encoding genes were genotyped, and phylogenetic groupings were determined by multiplex polymerase chain reaction (PCR). The presence of mcr-1 was also confirmed by PCR and sequencing. Results A total of 175 ESBL-producing E. coli isolated before and up to 2 weeks after traveling to Vietnam were analyzed. Genotyping of ESBL-producing isolates showed that blaCTX-M-1/blaTEM (27.7%) and blaCTX-M-9 (45.9%) were the most prevalent genotypes, while the most frequently detected phylogenetic group was D (41.9%) followed by B2 (23.0%). In a significant number of travel events, travelers brought ESBL-producing E. coli back to Japan and three events by three travelers carried mcr-1. ESBL-producing E. coli isolates harboring mcr-1 were identified as those carrying both blaCTX-M-14 or blaCTX-M-55 and mcr-1. Conclusion Using Vietnam as an example, we have shown that even a short-term trip to some countries may result in ESBL-producing mcr-1-positive E. coli carriage by international travelers.
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Affiliation(s)
- Tatsuya Nakayama
- Center for Global Initiatives, Osaka University, Suita, Osaka, Japan.,Division of Biomedical Food Research, National Institute of Health Science, Kawasaki, Kanagawa, Japan
| | - Yuko Kumeda
- Center for Microorganism Control, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Ryuji Kawahara
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Takahiro Yamaguchi
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Yoshimasa Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
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26
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Liakopoulos A, van den Bunt G, Geurts Y, Bootsma MCJ, Toleman M, Ceccarelli D, van Pelt W, Mevius DJ. High Prevalence of Intra-Familial Co-colonization by Extended-Spectrum Cephalosporin Resistant Enterobacteriaceae in Preschool Children and Their Parents in Dutch Households. Front Microbiol 2018. [PMID: 29515562 PMCID: PMC5826366 DOI: 10.3389/fmicb.2018.00293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Extended-spectrum cephalosporin-resistant (ESCR) Enterobacteriaceae pose a serious infection control challenge for public health. The emergence of the ESCR phenotype is mostly facilitated by plasmid-mediated horizontal extended-spectrum β-lactamases (ESBLs) and AmpC gene transfer within Enterobacteriaceae. Current data regarding the plasmid contribution to this emergence within the Dutch human population is limited. Hence, the aim of this study was to gain insight into the role of plasmids in the dissemination of ESBL/AmpC genes inside Dutch households with preschool children and precisely delineate co-colonization. In 87 ESCREnterobacteriaceae from fecal samples of parents and preschool children within 66 Dutch households, genomic localization, plasmid type and insertion sequences linked to ESBL/AmpC genes were determined. Chromosomal location of ESBL/AmpC genes was confirmed when needed. An epidemiologically relevant subset of the isolates based on household co-carriage was assessed by Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis for genetic relatedness. The narrow-host range I1α and F plasmids were the major facilitators of ESBL/AmpC-gene dissemination. Interestingly, we documented a relatively high occurrence of chromosomal integration of typically plasmid-encoded ESBL/AmpC-genes. A high diversity of non-epidemic Escherichia coli sequence types (STs) was revealed; the predominant STs belonged to the pandemic lineages of extraintestinal pathogenic E. coli ST131 and ST69. Intra-familiar co-carriage by identical ESCREnterobacteriaceae was documented in 7 households compared to 14 based on sole gene typing, as previously reported. Co-carriage was more frequent than expected based on pure chance, suggesting clonal transmission between children and parents within the household.
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Affiliation(s)
- Apostolos Liakopoulos
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Gerrita van den Bunt
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Yvon Geurts
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Martin C J Bootsma
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Mathematics, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Mark Toleman
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Wilfrid van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Dik J Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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27
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Guenther S, Semmler T, Stubbe A, Stubbe M, Wieler LH, Schaufler K. Chromosomally encoded ESBL genes in Escherichia coli of ST38 from Mongolian wild birds. J Antimicrob Chemother 2018; 72:1310-1313. [PMID: 28158613 DOI: 10.1093/jac/dkx006] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/04/2017] [Indexed: 01/16/2023] Open
Abstract
Objectives ESBL genes in Escherichia coli are mainly plasmid encoded, although recent studies have also shown chromosomal integration, e.g. in clinical E. coli isolates of ST38. As ESBL-producing E. coli are also found in non-clinical settings, we were interested in determining whether chromosomally integrated ESBL genes occur in ST38 isolates from non-clinical habitats, e.g. wildlife. Methods Four ESBL-producing E. coli isolates of ST38 originating from Mongolian birds of prey sampled in 2015 were subjected to a detailed analysis in terms of phenotypic resistance, plasmid profiling and WGS, followed by the determination of genotypic resistance factors including the chromosomal integration of ESBL and carbapenemase genes. Results Results based on phenotypic and genotypic plasmid profiling, contiguous sequence (contig) sizes and PCR analysis of flanking insertion site regions showed that three of four ST38 isolates harboured chromosomally encoded bla CTX-M genes of three different types ( bla CTX-M-14 , bla CTX-M-15 and bla CTX-M-24 ) that were inserted into three different chromosomal locations. A comparison of WGS data with ST38 isolates from a clinical outbreak in the UK indicated only low numbers of core-genome SNPs detected among one Mongolian wild bird isolate and eight clinical isolates from the UK. Conclusions The chromosomal integration of bla CTX-M genes in E. coli isolates of ST38 appears to be common and is likely independent of antimicrobial selective pressure in clinical environments. Our data corroborate the zoonotic potential of environmental isolates of ESBL-producing E. coli , which harbour stably integrated, chromosomally encoded resistance factors.
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Affiliation(s)
- Sebastian Guenther
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
| | | | - Annegret Stubbe
- Department of Zoology, Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 8, 06120 Halle, Germany
| | - Michael Stubbe
- Department of Zoology, Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 8, 06120 Halle, Germany
| | | | - Katharina Schaufler
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
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28
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Mohsin M, Raza S, Schaufler K, Roschanski N, Sarwar F, Semmler T, Schierack P, Guenther S. High Prevalence of CTX-M-15-Type ESBL-Producing E. coli from Migratory Avian Species in Pakistan. Front Microbiol 2017; 8:2476. [PMID: 29312186 PMCID: PMC5733096 DOI: 10.3389/fmicb.2017.02476] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/29/2017] [Indexed: 12/21/2022] Open
Abstract
The increased presence of clinically relevant multidrug resistant bacteria in natural environments is an emerging challenge for global health care. Little is known regarding the occurrence of extended-spectrum beta-lactamase producing Escherichia coli (ESBL-E. coli) from environmental sentinels in Pakistan. The goal of the current study was to gain insights into the prevalence and phylogenetic relationships of ESBL-E. coli recovered from wild birds in Pakistan during winter migration. After initial screening of fecal samples on selective chromogenic agar, ESBL-E.coli were analyzed phenotypically using the Vitek-2 automated system. Genotypic characterization was performed using whole genome sequencing (WGS) followed by an in-depth in silico analysis. Of 150 birds screened, 26 (17.3%) were fecal carriers of ESBL-E. coli. Of these, 88.4% isolates exhibited multidrug resistance (MDR) phenotypes. Resistance to cefotaxime, ceftazidime, ampicillin, doxycycline, tetracycline and sulfamethoxazole/trimethoprim (CTX-CAZ-AM-DC-TE-SXT) represented the most common pattern of MDR (76.9%). WGS data analysis found blaCTX-M-15 as the predominant ESBL genotype (92.3%). Other genes encoding resistance to sulfonamides (sul1/sul2/sul3), aminoglycosides (strA, strB, aadA1, aadA2, aadA5, aac(3)-IId-like, aac(3)-IVa-like and aph(4)-Ia), trimethoprim (dfrA14 or dfrA17), tetracyclines [tet(A)/tet(B)], and fluoroquinolones (qnrS1) were detected commonly, often encoded on IncF-type plasmids (76.9%). ESBL-E. coli were assigned to 17 different sequence types (STs) of which ST10 and ST7097 (4 isolates each) were the most abundant followed by ST4720, ST93, and ST1139 (2 isolates each). Core-genome phylogeny of the isolates found low numbers (0-29) of single nucleotide polymorphisms (SNPs) in isolates belonged to ST7097 originated from two different locations (Chashma barrage and Rasul barrage). Similar trends were found among isolates belong to ST1139. In addition, WGS-based plasmid typing and S1-digestion found plasmids of the same pMLST type (IncF[F-:A-:B53]) and similar sizes in different bacterial and avian hosts suggesting horizontal gene transfer as another possibility for the spread of ESBL-E. coli in avian wildlife in Pakistan.
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Affiliation(s)
- Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Shahbaz Raza
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Katharina Schaufler
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Nicole Roschanski
- Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Fatima Sarwar
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Torsten Semmler
- NG 1-Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Peter Schierack
- Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Sebastian Guenther
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
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29
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Irrgang A, Falgenhauer L, Fischer J, Ghosh H, Guiral E, Guerra B, Schmoger S, Imirzalioglu C, Chakraborty T, Hammerl JA, Käsbohrer A. CTX-M-15-Producing E. coli Isolates from Food Products in Germany Are Mainly Associated with an IncF-Type Plasmid and Belong to Two Predominant Clonal E. coli Lineages. Front Microbiol 2017; 8:2318. [PMID: 29209306 PMCID: PMC5702323 DOI: 10.3389/fmicb.2017.02318] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 11/09/2017] [Indexed: 01/06/2023] Open
Abstract
Extended-spectrum beta-lactamases (ESBL) mediating resistance to 3rd generation cephalosporins are a major public health issue. As food may be a vehicle in the spread of ESLB-producing bacteria, a study on the occurrence of cephalosporin-resistantu Escherichia coli in food was initiated. A total of 404 ESBL-producing isolates were obtained from animal-derived food samples (e.g., poultry products, pork, beef and raw milk) between 2011 and 2013. As CTX-M-15 is the most abundant enzyme in ESBL-producing E. coli causing human infections, this study focusses on E. coli isolates from food samples harboring the blaCTX-M-15 gene. The blaCTX-M-15 gene was detected in 5.2% (n = 21) of all isolates. Molecular analyses revealed a phylogenetic group A ST167 clone that was repeatedly isolated from raw milk and beef samples over a period of 6 months. The analyses indicate that spread of CTX-M-15-producing E. coli in German food samples were associated with a multireplicon IncF (FIA FIB FII) plasmid and additional antimicrobial resistance genes such as aac(6)-Ib-cr, blaOXA-1, catB3, different tet-variants as well as a class 1 integron with an aadA5/dfrA17 gene cassette. In addition, four phylogenetic group A ST410 isolates were detected. Three of them carried a chromosomal copy of the blaCTX-M-15 gene and a single isolate with the gene on a 90 kb IncF plasmid. The blaCTX-M-15 gene was always associated with the ISEcp1 element. In conclusion, CTX-M-15-producing E. coli were detected in German food samples. Among isolates of different matrices, two prominent clonal lineages, namely A-ST167 and A-ST410, were identified. These lineages may be important for the foodborne dissemination of CTX-M-15-producing E. coli in Germany. Interestingly, these clonal lineages were reported to be widely distributed and especially prevalent in isolates from humans and livestock. Transmission of CTX-M-15-harboring isolates from food-producing animals to food appears probable, as isolates obtained from livestock and food samples within the same time period exhibit comparable characteristics as compared to isolates detected from human. However, the routes and direction of transmission need further investigation.
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Affiliation(s)
- Alexandra Irrgang
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Jennie Fischer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Hiren Ghosh
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Elisabet Guiral
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Beatriz Guerra
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,European Food Safety Authority, Parma, Italy
| | - Silvia Schmoger
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Jens A Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annemarie Käsbohrer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Institute of Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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30
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Rojas LJ, Wright MS, De La Cadena E, Motoa G, Hujer KM, Villegas MV, Adams MD, Bonomo RA. Initial Assessment of the Molecular Epidemiology of blaNDM-1 in Colombia. Antimicrob Agents Chemother 2016; 60:4346-50. [PMID: 27067339 PMCID: PMC4914651 DOI: 10.1128/aac.03072-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/07/2016] [Indexed: 01/11/2023] Open
Abstract
We report complete genome sequences of four blaNDM-1-harboring Gram-negative multidrug-resistant (MDR) isolates from Colombia. The blaNDM-1 genes were located on 193-kb Inc FIA, 178-kb Inc A/C2, and 47-kb (unknown Inc type) plasmids. Multilocus sequence typing (MLST) revealed that these isolates belong to sequence type 10 (ST10) (Escherichia coli), ST392 (Klebsiella pneumoniae), and ST322 and ST464 (Acinetobacter baumannii and Acinetobacter nosocomialis, respectively). Our analysis identified that the Inc A/C2 plasmid in E. coli contained a novel complex transposon (Tn125 and Tn5393 with three copies of blaNDM-1) and a recombination "hot spot" for the acquisition of new resistance determinants.
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Affiliation(s)
- Laura J Rojas
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | | | - Elsa De La Cadena
- International Center for Medical Research and Training, CIDEIM, Cali, Colombia
| | - Gabriel Motoa
- International Center for Medical Research and Training, CIDEIM, Cali, Colombia
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Maria V Villegas
- International Center for Medical Research and Training, CIDEIM, Cali, Colombia
| | - Mark D Adams
- J. Craig Venter Institute, La Jolla, California, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
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31
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High Prevalence of Chromosomal blaCTX-M-14 in Escherichia coli Isolates Possessing blaCTX-M-14. Antimicrob Agents Chemother 2016; 60:2582-4. [PMID: 26810652 DOI: 10.1128/aac.00108-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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32
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Zhou K, Lokate M, Deurenberg RH, Arends J, Lo-Ten Foe J, Grundmann H, Rossen JWA, Friedrich AW. Characterization of a CTX-M-15 Producing Klebsiella Pneumoniae Outbreak Strain Assigned to a Novel Sequence Type (1427). Front Microbiol 2015; 6:1250. [PMID: 26617589 PMCID: PMC4639626 DOI: 10.3389/fmicb.2015.01250] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/27/2015] [Indexed: 12/01/2022] Open
Abstract
Extended-spectrum -lactamase producing Klebsiella pneumoniae have emerged as one of the major nosocomial pathogens. Between July and September 2012, a CTX-M-15 producing K. pneumoniae caused an outbreak in a university hospital in the Netherlands. The outbreak isolates were characterized and assigned to a novel sequence type (ST1427). An epidemiological link between affected patients was supported by patient contact tracing and whole-genome phylogenetic analysis. Intra-strain polymorphism was detected among multiple isolates obtained from different body sites of the index patient, which may relate to antibiotic treatment and/or host adaptation. Environmental contamination caused by the outbreak clone was found in the patient rooms even on medical equipment. The novel clone was not closely related to any known endemic/epidemic clone, but carried a set of a plasmid-borne resistance genes [blaCTX−M−15, blaTEM−1, blaOXA−1, aac(6′)-Ib-cr, qnrB1, tetA(A), aac(3)-II]. Analysis of its virulence factors revealed a previously uncharacterized capsular biosynthesis region and two uncharacterized fimbriae gene clusters, and suggested that the new clone was not hypervirulent. To our knowledge, this is the first outbreak report of K. pneumoniae ST1427, and our study could be of help to understand the features of this newly emerging clone.
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Affiliation(s)
- Kai Zhou
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen Groningen, Netherlands ; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University Hangzhou, China ; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases Hangzhou, China
| | - Mariëtte Lokate
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Ruud H Deurenberg
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Jan Arends
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Jerome Lo-Ten Foe
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Hajo Grundmann
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
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Carriage of Escherichia coli Producing CTX-M-Type Extended-Spectrum β-Lactamase in Healthy Vietnamese Individuals. Antimicrob Agents Chemother 2015. [PMID: 26195526 DOI: 10.1128/aac.00776-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Healthy carriage of CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli was examined by thrice collecting fecal samples from the same 199 healthy Vietnamese subjects every 6 months. Using pulsed-field gel electrophoresis (PFGE), identical PFGE patterns throughout the three samplings were not observed, although prevalence of E. coli in the subjects was around 50% in the three samplings. Our results suggested a short carriage period of the CTX-M-type ESBL-producing E. coli in healthy Vietnamese subjects.
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Abstract
In 2008, a previously unknown Escherichia coli clonal group, sequence type 131 (ST131), was identified on three continents. Today, ST131 is the predominant E. coli lineage among extraintestinal pathogenic E. coli (ExPEC) isolates worldwide. Retrospective studies have suggested that it may originally have risen to prominence as early as 2003. Unlike other classical group B2 ExPEC isolates, ST131 isolates are commonly reported to produce extended-spectrum β-lactamases, such as CTX-M-15, and almost all are resistant to fluoroquinolones. Moreover, ST131 E. coli isolates are considered to be truly pathogenic, due to the spectrum of infections they cause in both community and hospital settings and the large number of virulence-associated genes they contain. ST131 isolates therefore seem to contradict the widely held view that high levels of antimicrobial resistance are necessarily associated with a fitness cost leading to a decrease in pathogenesis. Six years after the first description of E. coli ST131, this review outlines the principal traits of ST131 clonal group isolates, based on the growing body of published data, and highlights what is currently known and what we need to find out to provide public health authorities with better information to help combat ST131.
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Ferreira JC, Penha Filho RAC, Andrade LN, Berchieri A, Darini ALC. Detection of chromosomal bla(CTX-M-2) in diverse Escherichia coli isolates from healthy broiler chickens. Clin Microbiol Infect 2014; 20:O623-6. [PMID: 24438126 DOI: 10.1111/1469-0691.12531] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 11/27/2022]
Abstract
The rise of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in food-producing animals is a growing concern for public health. We investigated ESBL producers isolated from broiler chickens in Brazil and characterized 19 CTX-M-2-producing E. coli. The ISCR1 was detected upstream of the chromosome-located gene bla(CTX-M-2), associated with sul-1 type integron structure. CTX-M-2-producing E. coli exhibited different PFGE-types and phylogenetic groups, showing a non-clonal dissemination. The sequence types found (ST93, ST155 and ST2309) have been associated with humans and animals worldwide. Herein, we report the chromosomal location of bla(CTX-M-2) on E. coli, highlighting the risks of multidrug-resistant bacteria in food-producing animals.
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Affiliation(s)
- J C Ferreira
- School of Pharmaceutical Sciences of Ribeirão Preto - São Paulo University (USP), Ribeirão Preto, SP, Brazil
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