1
|
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.
Collapse
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
| |
Collapse
|
2
|
Blaikie JM, Sapula SA, Siderius NL, Hart BJ, Amsalu A, Leong LE, Warner MS, Venter H. Resistome Analysis of Klebsiella pneumoniae Complex from Residential Aged Care Facilities Demonstrates Intra-facility Clonal Spread of Multidrug-Resistant Isolates. Microorganisms 2024; 12:751. [PMID: 38674695 PMCID: PMC11051875 DOI: 10.3390/microorganisms12040751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Antimicrobial-resistant Klebsiella pneumoniae is one of the predominant pathogens in healthcare settings. However, the prevalence and resistome of this organism within residential aged care facilities (RACFs), which are potential hotspots for antimicrobial resistance, remain unexplored. Here, we provide a phenotypic and molecular characterization of antimicrobial-resistant K. pneumoniae isolated from RACFs. K. pneumoniae was isolated from urine, faecal and wastewater samples and facility swabs. The antimicrobial susceptibility profiles of all the isolates were determined and the genomic basis for resistance was explored with whole-genome sequencing on a subset of isolates. A total of 147 K. pneumoniae were isolated, displaying resistance against multiple antimicrobials. Genotypic analysis revealed the presence of beta-lactamases and the ciprofloxacin-resistance determinant QnrB4 but failed to confirm the basis for the observed cephalosporin resistance. Clonal spread of the multidrug-resistant, widely disseminated sequence types 323 and 661 was observed. This study was the first to examine the resistome of K. pneumoniae isolates from RACFs and demonstrated a complexity between genotypic and phenotypic antimicrobial resistance. The intra-facility dissemination and persistence of multidrug-resistant clones is concerning, given that residents are particularly vulnerable to antimicrobial resistant infections, and it highlights the need for continued surveillance and interventions to reduce the risk of outbreaks.
Collapse
Affiliation(s)
- Jack M. Blaikie
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Sylvia A. Sapula
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Naomi L. Siderius
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Bradley J. Hart
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Anteneh Amsalu
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
- Department of Medical Microbiology, University of Gondar, Gondar 196, Ethiopia
| | - Lex E.X. Leong
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA 5000, Australia;
| | - Morgyn S. Warner
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA 5000, Australia;
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
- Infectious Diseases Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Henrietta Venter
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| |
Collapse
|
3
|
Mutua JM, Njeru JM, Musyoki AM. Extended-spectrum β-lactamase- producing gram-negative bacterial infections in severely ill COVID-19 patients admitted in a national referral hospital, Kenya. Ann Clin Microbiol Antimicrob 2023; 22:91. [PMID: 37838665 PMCID: PMC10576885 DOI: 10.1186/s12941-023-00641-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Bacterial infections in COVID-19 patients, especially those caused by multidrug-resistant gram-negative strains, are associated with increased morbidity, hospital stay and mortality. However, there is limited data on the epidemiology of extended-spectrum β-lactamase (ESBL)-producing bacteria in COVID-19 patients. Here, we assessed the prevalence and the factors associated with ESBL-producing gram-negative bacterial (GNB) infections among severely ill COVID-19 patients admitted in Kenyatta National Hospital (KNH), Kenya. METHODS We adopted a descriptive cross-sectional study design for patients admitted between October 2021 and February 2022, purposively recruiting 120 SARS-CoV- 2 infected participants based on clinical presentation. Demographics and clinical characteristics data were collected using structured questionnaires and case report forms. Clinical samples were collected and analyzed by standard microbiological methods in the KNH Microbiology laboratory and the Centre for Microbiology Research, Kenya Medical Research Institute. RESULTS GNB infections prevalence was 40.8%, majorly caused by ESBL-producers (67.3%) predominated by Klebsiella pneumoniae (45.5%). Generally, 73% of the ESBL producers harboured our target ESBL genes, mainly CTX-M-type (59%, 17/29) in K. pneumoniae (76.9%, 20/26). GNB harbouring TEM-type (83%, 10/12) and SHV-type (100%, 7/7) genes showed ESBLs phenotypes and inhibitor resistance, mainly involving clavulanate, but most of them remained susceptible to tazobactam (60%, 6/10). SHV-type genes carrying ESBL producers showed resistance to both cefotaxime (CTX) and ceftazidime (CAZ) (K. pneumoniae), CAZ (E. coli) or CTX (E. cloacae complex and K. pneumoniae). About 87% (20/23) of isolates encoding CTX-M-type β-lactamases displayed CTX/ceftriaxone (CRO) resistance phenotype. About 42% of isolates with CTX-M-type β-lactamases only hydrolyzed ceftazidime (CAZ). Isolates with OXA-type β-lactamases were resistant to CTX, CAZ, CRO, cefepime and aztreonam. Patients with comorbidities were 10 times more likely to have an ESBL-producing GNB infection (aOR = 9.86, 95%CI 1.30 - 74.63, p = 0.003). CONCLUSION We report a high prevalence of ESBL-GNB infections in severely ill COVID-19 patients, predominantly due to Klebsiella pneumoniae harbouring CTX-M type ESBL genes. The patient's underlying comorbidities increased the risk of ESBL-producing GNB infection. In COVID-19 pandemic, enhanced systematic and continuous surveillance of ESBL-producing GNB, strict adherence to infection control measures and antimicrobial stewardship policies are warranted in the current study setting.
Collapse
Affiliation(s)
- Jeniffer Munyiva Mutua
- Department of Laboratory Medicine, Kenyatta National Hospital, 20723-00202, Nairobi, Kenya.
- Department of Medical Laboratory Sciences, Kenyatta University, 43844-00100, Nairobi, Kenya.
| | - John Mwaniki Njeru
- Centre for Microbiology Research, Kenya Medical Research Institute, 19464-00200, Nairobi, Kenya
| | - Abednego Moki Musyoki
- Department of Medical Laboratory Sciences, Kenyatta University, 43844-00100, Nairobi, Kenya
| |
Collapse
|
4
|
Zhang S, Guo X, Wang Y, Zhong Z, Wang M, Jia R, Chen S, Liu M, Zhu D, Zhao X, Wu Y, Yang Q, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A. Implications of different waterfowl farming on cephalosporin resistance: Investigating the role of bla CTX-M-55. Poult Sci 2023; 102:102929. [PMID: 37562134 PMCID: PMC10432832 DOI: 10.1016/j.psj.2023.102929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023] Open
Abstract
We investigated the cephalosporin resistance of Escherichia coli from waterfowl among different breeding mode farms. In 2021, we isolated 200 strains of E. coli from waterfowl feces samples collected from Sichuan, Heilongjiang, and Anhui provinces. The key findings are: Out of the 200 strains, 80, 80, and 40 strains were isolated from waterfowl feces samples in intensive, courtyard, and outdoor breeding mode farms, respectively. The overall positive rate of the ESBL phenotype, detecting by the double disk diffusion method, was 68.00% (136/200). In particular, the rates for intensive, courtyard, and outdoor breeding modes were 98.75%, 36.25%, and 70.00%, respectively. Results of MIC test showed drug resistance rates in the intensive breeding mode: 100.00% for cephalothin, 38.75% for cefoxitin, 100.00% for cefotaxime, and 100.00% for cefepime. In courtyard breeding mode, the corresponding rates were 100.00%, 40.00%, 63.75%, and 45.00%, respectively. In outdoor breeding mode, the corresponding rates were 100.00%, 52.50%, 82.50%, and 77.50%, respectively. The PCR results for blaCTX-M, blaTEM, blaOXA, and blaSHV showed the detection rate of blaCTX-M was highest at 75.50%, with blaCTX-M-55 is the main subtype gene, followed by blaTEM at 73.50%. We screened 58 donor strains carrying blaCTX-M-55, including 52 strains from the intensive breeding mode. These donor bacteria can transfer different plasmids to recipient E. coli J53, resulting in recipient bacteria acquiring cephalosporin resistance, and the conjugational transfer frequency ranged from 1.01 × 10-5 to 6.56 × 10-2. The transferred plasmids remained stable in recipient bacteria for up to several days without significant adaptation costs observed. During molecular typing of E. coli with conjugational transfer ability, the blaCTX-M-55 was found to be widely present in different ST strains with several phylogenetic groups. In summary, cephalosporin resistance of E. coli carried by waterfowl birds in intensive breeding mode farm was significantly higher than in courtyard and outdoor mode farms. The blaCTX-M-55 subtype gene was the prevalent ARGs and can be horizontally transferred through plasmids, which plays a key role in the spread of cephalosporin drug resistance.
Collapse
Affiliation(s)
- Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Xiangyuan Guo
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yuwei Wang
- Mianyang Academy of Agricultural Sciences, Mianyang 621023, P.R. China
| | - Zhijun Zhong
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Ying Wu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Qiao Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Juan Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Xumin Ou
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Sai Mao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Qun Gao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Di Sun
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, P.R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R. China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Chengdu 611130, P.R. China.
| |
Collapse
|
5
|
Sun J, Chikunova A, Boyle AL, Voskamp P, Timmer M, Ubbink M. Enhanced activity against a third-generation cephalosporin by destabilization of the active site of a class A beta-lactamase. Int J Biol Macromol 2023; 250:126160. [PMID: 37549761 DOI: 10.1016/j.ijbiomac.2023.126160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/10/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
The β-lactamase BlaC conveys resistance to a broad spectrum of β-lactam antibiotics to its host Mycobacterium tuberculosis but poorly hydrolyzes third-generation cephalosporins, such as ceftazidime. Variants of other β-lactamases have been reported to gain activity against ceftazidime at the cost of the native activity. To understand this trade-off, laboratory evolution was performed, screening for enhanced ceftazidime activity. The variant BlaC Pro167Ser shows faster breakdown of ceftazidime, poor hydrolysis of ampicillin and only moderately reduced activity against nitrocefin. NMR spectroscopy, crystallography and kinetic assays demonstrate that the resting state of BlaC P167S exists in an open and a closed state. The open state is more active in the hydrolysis of ceftazidime. In this state the catalytic residue Glu166, generally believed to be involved in the activation of the water molecule required for deacylation, is rotated away from the active site, suggesting it plays no role in the hydrolysis of ceftazidime. In the closed state, deacylation of the BlaC-ceftazidime adduct is slow, while hydrolysis of nitrocefin, which requires the presence of Glu166 in the active site, is barely affected, providing a structural explanation for the trade-off in activities.
Collapse
Affiliation(s)
- Jing Sun
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Aleksandra Chikunova
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Aimee L Boyle
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Patrick Voskamp
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Monika Timmer
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Marcellus Ubbink
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.
| |
Collapse
|
6
|
Yang J, Zhang K, Ding C, Wang S, Wu W, Liu X. Exploring multidrug-resistant Klebsiella pneumoniae antimicrobial resistance mechanisms through whole genome sequencing analysis. BMC Microbiol 2023; 23:245. [PMID: 37660028 PMCID: PMC10474722 DOI: 10.1186/s12866-023-02974-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/08/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND Antibiotic-resistant Klebsiella pneumoniae has emerged as a critical public health threat worldwide. Understanding the antimicrobial resistance mechanisms of multidrug-resistant K. pneumoniae (MDR-Kp) and its prevalence in time and space would provide clinical significance for managing pathogen infection. METHODS Eighteen clinical MDR-Kp strains were analyzed by whole genome sequencing (WGS), and the antimicrobial resistance genes and associated resistance mechanisms were compared with results obtained from the conventional microbiological test (CMT). The sequence homology across strains in our study and those previously collected over time from a wide geographical region was assessed by phylogenetic analysis. RESULTS MDR-Kp strains were collected from eighteen patients who had received empirical treatment before strain collection, with sputum (83.3%, 15/18) being the primary source of clinical samples. The commonly received treatments include β-lactamase inhibitors (55.6%, 10/18) and carbapenems (50%, 9/18). Using CMT, we found that all 18 strains were resistant to aztreonam and ciprofloxacin, while 14 (77.8%) showed resistance to carbapenem. Polymyxin B and tigecycline were the only antibiotics to which MDR-Kp strains were sensitive. A total of 42 antimicrobial resistance mechanisms were identified by WGS, surpassing the 40 detected by the conventional method, with 25 mechanisms shared between the two techniques. Despite a 100% accuracy rate of WGS in detecting penicillin-resistant strains, the accuracy in detecting cephalosporin-resistant strains was only at 60%. Among all resistance genes identified by WGS, Klebsiella pneumoniae carbapenemase-2 (KPC-2) was present in all 14 carbapenem-resistant strains. Phenotypic analysis indicated that sequence type (ST) 11 isolates were the primary cause of these MDR-Kp infections. Additionally, phylogenic clustering analysis, encompassing both the clinical and MDR-Kp strains previously reported in China, revealed four distinct subgroups. No significant difference was observed in the sequence homology between K. pneumoniae strains in our study and those previously collected in East China over time. CONCLUSION The application of WGS in identifying potential antimicrobial-resistant genes of MDR-Kp has demonstrated promising clinical significance. Comprehensive genomic information revealed by WGS holds the promise of guiding treatment decisions, enabling surveillance, and serving as a crucial asset in understanding antibiotic resistance.
Collapse
Affiliation(s)
- Jing Yang
- Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Kai Zhang
- Clinical Laboratory, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, No. 269, Daxue Road, Tongshan District, Xuzhou, 221002, Jiangsu, China
| | - Chen Ding
- Xuzhou Central Hospital, Xuzhou, 221009, Jiangsu, China
| | - Song Wang
- Dinfectome Inc, Nanjing, 210000, Jiangsu, China
| | - Weiwei Wu
- Dinfectome Inc, Nanjing, 210000, Jiangsu, China
| | - Xiangqun Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, No. 269, Daxue Road, Tongshan District, Xuzhou, 221002, Jiangsu, China.
| |
Collapse
|
7
|
Sarr H, Niang AA, Diop A, Mediannikov O, Zerrouki H, Diene SM, Lo S, Dia ML, Sow AI, Fenollar F, Rolain JM, Hadjadj L. The Emergence of Carbapenem- and Colistin-Resistant Enterobacteria in Senegal. Pathogens 2023; 12:974. [PMID: 37623934 PMCID: PMC10459028 DOI: 10.3390/pathogens12080974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Antibiotic resistance is a public health problem. The emergence of carbapenemase-producing Enterobacterales (CPE) infections is a concern, particularly in Senegal. (1) Methods: Between January 2019 and July 2022, 240 isolates of enterobacteria resistant to third-generation cephalosporins and imipenem from biological samples from Fann Hospital (Dakar) and Hôpital Paix (Ziguinchor) were selected. The isolates were identified by MALDI-TOF mass spectrometry, and susceptibility tests were performed by the disk diffusion method. Antibiotic-resistance genes for class A beta-lactamases, carbapenemases, and plasmid resistance to colistin resistance (mcr-1-8) were screened by RT-PCR. (2) Results: The 240 enterobacteria were composed of: Escherichia coli (60.83%), Klebsiella pneumoniae (21.67%), Enterobacter cloacae (13.75%), Citrobacter freundii (2.08%), Serratia marcescens (0.83%), Klebsiella aerogenes (0.42%), and Proteus mirabilis (0.42%). Class A beta-lactamase genes were found in 229 isolates (70.41% blaTEM, 37.5% blaSHV, 83.75% blaCTX-A, and 0.42% blaCTX-B). The carbapenemase genes blaOXA-48 and blaNDM were found in 25 isolates, including 14 isolates with blaOXA-48, 13 isolates with blaNDM, and 2 isolates with both genes simultaneously. The mcr-8 gene was found in one isolate of E. cloacae. (3) Conclusions: The epidemiology of antibiotic-resistance genes in enterobacteria in Senegal shows the emergence of CPEs. This phenomenon is worrying, and rigorous surveillance is necessary to avoid further spread.
Collapse
Affiliation(s)
- Habibou Sarr
- UFR des Sciences de la Santé, Université Assane Seck de Ziguinchor, Ziguinchor BP 523, Senegal;
- Unité de Bactériologie, Hôpital de la Paix de Ziguinchor, Ziguinchor BP 523, Senegal
- Faculté de Médecine et de Pharmacie, MEPHI IRD, APHM, Aix Marseille Université, 13005 Marseille, France; (O.M.); (H.Z.); (S.M.D.); (J.-M.R.)
- IHU Méditerranée Infection, 13005 Marseille, France;
| | - Aissatou Ahmet Niang
- Faculté de Médecine, Pharmacie et Odonto-Stomatologie, Université Cheikh-Anta-Diop, Dakar BP 5005, Senegal; (A.A.N.); (A.D.); (M.L.D.); (A.I.S.)
| | - Amadou Diop
- Faculté de Médecine, Pharmacie et Odonto-Stomatologie, Université Cheikh-Anta-Diop, Dakar BP 5005, Senegal; (A.A.N.); (A.D.); (M.L.D.); (A.I.S.)
| | - Oleg Mediannikov
- Faculté de Médecine et de Pharmacie, MEPHI IRD, APHM, Aix Marseille Université, 13005 Marseille, France; (O.M.); (H.Z.); (S.M.D.); (J.-M.R.)
- IHU Méditerranée Infection, 13005 Marseille, France;
| | - Hanane Zerrouki
- Faculté de Médecine et de Pharmacie, MEPHI IRD, APHM, Aix Marseille Université, 13005 Marseille, France; (O.M.); (H.Z.); (S.M.D.); (J.-M.R.)
- IHU Méditerranée Infection, 13005 Marseille, France;
| | - Seydina M. Diene
- Faculté de Médecine et de Pharmacie, MEPHI IRD, APHM, Aix Marseille Université, 13005 Marseille, France; (O.M.); (H.Z.); (S.M.D.); (J.-M.R.)
- IHU Méditerranée Infection, 13005 Marseille, France;
| | - Seynabou Lo
- UFR des Sciences de la Santé, Université Gaston Berger, Saint Louis BP 234, Senegal;
| | - Mouhamadou Lamine Dia
- Faculté de Médecine, Pharmacie et Odonto-Stomatologie, Université Cheikh-Anta-Diop, Dakar BP 5005, Senegal; (A.A.N.); (A.D.); (M.L.D.); (A.I.S.)
| | - Ahmad Iyane Sow
- Faculté de Médecine, Pharmacie et Odonto-Stomatologie, Université Cheikh-Anta-Diop, Dakar BP 5005, Senegal; (A.A.N.); (A.D.); (M.L.D.); (A.I.S.)
| | - Florence Fenollar
- IHU Méditerranée Infection, 13005 Marseille, France;
- VITROME, IRD, APHM, SSA, Aix Marseille Université, 13005 Marseille, France
| | - Jean-Marc Rolain
- Faculté de Médecine et de Pharmacie, MEPHI IRD, APHM, Aix Marseille Université, 13005 Marseille, France; (O.M.); (H.Z.); (S.M.D.); (J.-M.R.)
- IHU Méditerranée Infection, 13005 Marseille, France;
| | - Linda Hadjadj
- Faculté de Médecine et de Pharmacie, MEPHI IRD, APHM, Aix Marseille Université, 13005 Marseille, France; (O.M.); (H.Z.); (S.M.D.); (J.-M.R.)
- IHU Méditerranée Infection, 13005 Marseille, France;
| |
Collapse
|
8
|
Shao J, Dai H, Xu L, Zhu S, Zhu J, Fu H, Ge M, He X. Genomic Characteristics of Extended Spectrum β-Lactamase Producing Escherichia coli Isolates Recovered from a District Hospital in China. Infect Drug Resist 2023; 16:3589-3600. [PMID: 37309377 PMCID: PMC10257927 DOI: 10.2147/idr.s415373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/02/2023] [Indexed: 06/14/2023] Open
Abstract
Purpose The isolation rate of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is increasing, posing a challenge to clinical anti-infective therapy. This study aims to provide new insight into the genomic characteristics and antimicrobial resistance mechanisms of extended spectrum β-lactamase producing E. coli isolates recovered from a district hospital in China. Methods A total of 36 ESBL-producing E. coli isolates were collected from body fluid samples from a Chinese district hospital. All isolates were subjected to whole genome sequencing to identify their antimicrobial resistance genes, virulence genes, serotypes, sequence types, and phylogenetic relationships by BacWGSTdb 2.0 webserver. Results Among these isolates, all were resistant to cefazolin, cefotaxime, ceftriaxone, ampicillin, 24 (66.7%) were resistant to aztreonam, 16 (44.4%) were resistant to cefepime, and 15 were resistant (41.7%) to ceftazidime. The blaCTX-M gene was detected in all ESBL-producing E. coli isolates. Two isolates carrying two different types of blaCTX-M genes simultaneously. The carbapenem resistance gene blaKPC-2 was detected in one (2.8%) isolate. A total of 17 sequence types (STs) were found, with ST131 accounting for the majority (n =13; 36.1%). The most common serotype was O16:H5 associated with seven ST131 strains, followed by O25:H4/ST131 (n = 5) and O75:H5/ST1193 (n = 5). Evaluation of clonal relatedness revealed that all blaCTX-M gene-carrying E. coli had a difference of SNPs range from 7 to 79,198, which could be divided into four clusters. Only 7 SNPs could be found between EC266 and EC622, indicating that they are variants of the same clonal lineage. Conclusion This study investigated the genomic characteristics of ESBL-producing E. coli isolates recovered from a district hospital in China. Continuous surveillance of ESBL-producing E. coli infections is imperative to create efficient strategies for controlling the transmission of these multi-drug resistant bacteria in clinical and community settings.
Collapse
Affiliation(s)
- Jiayu Shao
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Hangdong Dai
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Liwei Xu
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Shuilong Zhu
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Jufang Zhu
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Hangyu Fu
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Minxia Ge
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Xianhong He
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| |
Collapse
|
9
|
Davidova-Gerzova L, Lausova J, Sukkar I, Nesporova K, Nechutna L, Vlkova K, Chudejova K, Krutova M, Palkovicova J, Kaspar J, Dolejska M. Hospital and community wastewater as a source of multidrug-resistant ESBL-producing Escherichia coli. Front Cell Infect Microbiol 2023; 13:1184081. [PMID: 37256105 PMCID: PMC10225658 DOI: 10.3389/fcimb.2023.1184081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023] Open
Abstract
Introduction Hospitals and wastewater are recognized hot spots for the selection and dissemination of antibiotic-resistant bacteria to the environment, but the total participation of hospitals in the spread of nosocomial pathogens to municipal wastewater treatment plants (WWTPs) and adjacent rivers had not previously been revealed. Methods We used a combination of culturing and whole-genome sequencing to explore the transmission routes of Escherichia coli from hospitalized patients suffering from urinary tract infections (UTI) via wastewater to the environment. Samples were collected in two periods in three locations (A, B, and C) and cultured on selective antibiotic-enhanced plates. Results In total, 408 E. coli isolates were obtained from patients with UTI (n=81), raw hospital sewage (n=73), WWTPs inflow (n=96)/outflow (n=106), and river upstream (n=21)/downstream (n=31) of WWTPs. The majority of the isolates produced extended-spectrum beta-lactamase (ESBL), mainly CTX-M-15, and showed multidrug resistance (MDR) profiles. Seven carbapenemase-producing isolates with GES-5 or OXA-244 were obtained in two locations from wastewater and river samples. Isolates were assigned to 74 different sequence types (ST), with the predominance of ST131 (n=80) found in all sources including rivers. Extraintestinal pathogenic lineages frequently found in hospital sewage (ST10, ST38, and ST69) were also found in river water. Despite generally high genetic diversity, phylogenetic analysis of ST10, ST295, and ST744 showed highly related isolates (SNP 0-18) from different sources, providing the evidence for the transmission of resistant strains through WWTPs to surface waters. Discussion Results of this study suggest that 1) UTI share a minor participation in hospitals wastewaters; 2) a high diversity of STs and phylogenetic groups in municipal wastewaters derive from the urban influence rather than hospitals; and 3) pathogenic lineages and bacteria with emerging resistance genotypes associated with hospitals spread into surface waters. Our study highlights the contribution of hospital and municipal wastewater to the transmission of ESBL- and carbapenemase-producing E. coli with MDR profiles to the environment.
Collapse
Affiliation(s)
- Lenka Davidova-Gerzova
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Jarmila Lausova
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Iva Sukkar
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Kristina Nesporova
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Lucie Nechutna
- Department of Microbiology, Faculty of Medicine and University Hospital Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Katerina Vlkova
- Department of Microbiology, Faculty of Medicine and University Hospital Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Katerina Chudejova
- Department of Microbiology, Faculty of Medicine and University Hospital Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Jana Palkovicova
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Jakub Kaspar
- Center of Cardiovascular and Transplant Surgery, St. Anne’s University Hospital Brno, Brno, Czechia
| | - Monika Dolejska
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czechia
| |
Collapse
|
10
|
Ma K, Zong Z. Resistance to aztreonam-avibactam due to CTX-M-15 in the presence of penicillin-binding protein 3 with extra amino acids in Escherichia coli. Front Microbiol 2022; 13:1047109. [PMID: 36406430 PMCID: PMC9674307 DOI: 10.3389/fmicb.2022.1047109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Aztreonam-avibactam is a promising combination to treat carbapenem-resistant Enterobacterales including coverage for metallo-β-lactamases. Escherichia coli strains resistant to aztreonam-avibactam have emerged but resistance mechanisms remain to be elucidated. We performed a study to investigate the mechanism for aztreonam-avibactam in a carbapenem-resistant Escherichia coli clinical strain. This strain was resistant to aztreonam-avibactam (aztreonam MIC, 16 mg/L in the presence of 4 mg/L avibactam). Whole genome sequencing revealed that the strain carried metallo-β-lactamase gene blaNDM-4 and the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-15 and had a YRIK four amino acid insertion in penicillin-binding protein 3 (PBP3). blaCTX-M-15 was cloned into pET-28a(+), followed by the transformation, with the gene, of E. coli strain 035125∆pCMY42 possessing the YRIK insertion in PBP3 and strain BL21 with the wildtype PBP3. blaCTX-M-14, another common ESBL gene, and blaCTX-M-199, a hybrid of blaCTX-M-14 and blaCTX-M-15 were also individually cloned into both E. coli strains for comparison. Aztreonam-avibactam resistance was only observed in the E. coli strains with the YRIK insertion in PBP3 that produced CTX-M-15 or its hybrid enzyme CTX-M-199. Checkerboard titration assays were performed to determine the synergistic effects between aztreonam-avibactam and ceftazidime or meropenem. Doubling avibactam concentration in vitro reversed aztreonam-avibactam resistance, while the combination of aztreonam-avibactam and ceftazidime or meropenem did not. In conclusion, CTX-M enzymes with activity against aztreonam, (e.g., CTX-M-15 and CTX-M-199), can confer resistance in the combination of PBP3 with YRIK insertions in metallo-β-lactamase-producing carbapenem-resistant E. coli. Doubling the concentration of avibactam may overcome such resistance.
Collapse
Affiliation(s)
- Ke Ma
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
- *Correspondence: Zhiyong Zong,
| |
Collapse
|
11
|
Zhao H, He Z, Li Y, Sun B. Epidemiology of carbapenem-resistant Klebsiella pneumoniae ST15 of producing KPC-2, SHV-106 and CTX-M-15 in Anhui, China. BMC Microbiol 2022; 22:262. [PMID: 36319965 PMCID: PMC9624029 DOI: 10.1186/s12866-022-02672-1] [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: 07/27/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022] Open
Abstract
Background: It is well known that carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a more problematic public health issue due to its widespread spread worldwide. In China, ST11-type CRKP is the most prevalent CRKP, but ST15-type CRKP, a recently prevalent high-risk clone, has emerged widely throughout China, posing a serious public health risk. Therefore, we conducted an epidemiological of an outbreak of ST15 CRKP of producing CTX-M-15, KPC-2 and SHV-106 in a tertiary hospital in Anhui, China, to Understanding the potential risks of the current STT15 CRKP outbreak. Results: From July 2021 to December 2021, 13 ST15 CRKP isolates were identified by collecting non-repeated clinical multidrug-resistant isolates, with all capsular typing of serotype KL19. All ST15 CRKP isolates were resistant to cephalosporins, carbapenems and quinolones, but were sensitive to amikacin, tigecycline and polymyxin B. In addition, isolates carried blaSHV−106 (100%), blaKPC−2 (69%), blaCTX−M−15 (69%), blaTEM−1B (69%), blaOXA−1 (62%) and blaLAP−2 (8%), as well as iron chelators (iutA, ybt, fyuA, ent, fepA, irp1, irp2, 100%) were detected. In phenotyping experiments, all ST15 CRKP exhibited lower growth rates than NTUH-K2044, and all ST15 CRKP did not exhibit mucoviscositty characteristics. However, in the Galleria mellonella infection model, isolates 21081212, 21081241 and 21091216 were more lethal than the hypervirulent isolates NTUH-K2044. Sequencing results showed that the genetic environment surrounding the genes blaSHV−106, blaKPC−2, blaCTX−M−15, blaOXA−1 and blaTEM−1B were all identical in the ST15 CRKP isolates. Phylogenetic analysis showed that 13 ST15 CRKP isolates were divided into three subgroups, and when placed in global analysis, 10 of them were highly homologous to isolates from Jiangsu, two were highly homologous to isolates from Zhejiang, and one was homologous to an isolate from an unlabelled region. Conclusion: Our research shows that ST15 CRKP, which carries multiple β-lactamases genes and siderophores-encoding genes, may be evolving to hypervirulence and may have spread widely in localised areas. Therefore, environmental surveillance and clinical infection control in hospitals should be strengthened to prevent further spread of ST15 CRKP. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02672-1.
Collapse
Affiliation(s)
- Hang Zhao
- grid.443847.80000 0001 0805 3594College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Zhien He
- grid.59053.3a0000000121679639Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui China ,grid.59053.3a0000000121679639School of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Yujie Li
- grid.59053.3a0000000121679639Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui China ,grid.59053.3a0000000121679639School of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Baolin Sun
- grid.59053.3a0000000121679639Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui China ,grid.59053.3a0000000121679639School of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui China
| |
Collapse
|
12
|
Escherichia coli Isolated from Vegans, Vegetarians and Omnivores: Antibiotic Resistance, Virulence Factors, Pathogenicity Islands and Phylogenetic Classification. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13040058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pathogenic strains of Escherichia coli have acquired virulence factors, which confer an increased ability to cause a broad spectrum of enteric diseases and extraintestinal infections. The aim of this study was to analyze the antimicrobial resistance profile of and the presence of virulence-associated genes (VAGs) in E. coli fecal isolates from omnivores, vegetarians and vegans. A control group of 60 isolates from omnivores, as well as a study group with 41 isolates from vegetarians and 17 from vegans, were analyzed. Isolates from both groups showed a high rate of resistance to ampicillin, amoxicillin-clavulanic acid and nalidixic acid, and some of them were positive for the ESBL test (12% of isolates from vegetarians/vegans and 5% of isolates from omnivores). The most predominant VAGs detected in isolates from omnivores were fimH (70%), iutA (32%), fyuA (32%) and traT (32%), while among isolates from vegetarians or vegans, the most predominant were traT (62%), kpsMT k1 (28%) and iutA (22%). Most isolates from omnivores (55%) were positive for PAI I536, while most of those from vegetarians/vegans (59%) were positive for PAI IV536. Phylogenetic group A, composed of commensal non-pathogenic isolates that survive in the intestinal tract, was the most prevalent in both control and study groups. Some VAGs were found in only one of the groups, such as the pathogenicity island PAI III536, found in 12% of the isolates from omnivores, while the kpsMT III gene (15%) was detected only among isolates from vegetarians/vegans. Interestingly, this gene codes for a polysaccharide capsule found mainly in E. coli isolates causing intestinal infections, including EPEC, ETEC and EHEC. Finally, our results show that there were no advantages in vegetarian or vegan diets compared to the omnivorous diet, as in both groups we detected isolates harboring VAGs and displaying resistance to antibiotics, especially those most commonly used to treat urinary tract infections.
Collapse
|
13
|
Rossi MA, Palzkill T, Almeida FCL, Vila AJ. Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions. Mol Biol Evol 2022; 39:6711538. [PMID: 36136729 PMCID: PMC9547502 DOI: 10.1093/molbev/msac194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein evolution depends on the adaptation of these molecules to different functional challenges. This occurs by tuning their biochemical, biophysical, and structural traits through the accumulation of mutations. While the role of protein dynamics in biochemistry is well recognized, there are limited examples providing experimental evidence of the optimization of protein dynamics during evolution. Here we report an NMR study of four variants of the CTX-M β-lactamases, in which the interplay of two mutations outside the active site enhances the activity against a cephalosporin substrate, ceftazidime. The crystal structures of these enzymes do not account for this activity enhancement. By using NMR, here we show that the combination of these two mutations increases the backbone dynamics in a slow timescale and the exposure to the solvent of an otherwise buried β-sheet. The two mutations located in this β-sheet trigger conformational changes in loops located at the opposite side of the active site. We postulate that the most active variant explores alternative conformations that enable binding of the more challenging substrate ceftazidime. The impact of the mutations in the dynamics is context-dependent, in line with the epistatic effect observed in the catalytic activity of the different variants. These results reveal the existence of a dynamic network in CTX-M β-lactamases that has been exploited in evolution to provide a net gain-of-function, highlighting the role of alternative conformations in protein evolution.
Collapse
Affiliation(s)
- Maria-Agustina Rossi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo and Esmeralda, Rosario, Argentina
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, USA,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, USA
| | | | | |
Collapse
|
14
|
Habibzadeh N, Peeri Doghaheh H, Manouchehri Far M, Alimohammadi Asl H, Iranpour S, Arzanlou M. Fecal Carriage of Extended-Spectrum β-Lactamases and pAmpC Producing Enterobacterales in an Iranian Community: Prevalence, Risk Factors, Molecular Epidemiology, and Antibiotic Resistance. Microb Drug Resist 2022; 28:921-934. [PMID: 36067095 DOI: 10.1089/mdr.2021.0029] [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
This study aimed to determine the prevalence and risk factors associated with intestinal carriage of extended-spectrum β-lactamases producing Enterobacterales (ESBL-PE) and plasmid-mediated AmpC β-lactamase producing Enterobacterales (AmpC-PE) in healthy children in Ardabil, Iran. A total of 305 fecal samples were collected. Isolates underwent antimicrobial susceptibility testing, phenotypic and genotypic identification of β-lactamase production, and epidemiologic molecular typing. In total, 21.5%, 1.5%, and 1.2% of volunteers were extended-spectrum β-lactamase (ESBL)-, AmpC-, and simultaneous ESBL/AmpC-PE carriers, respectively. Escherichia coli was the predominant ESBL producing bacterium (70.2%) found in ESBL-PE colonized subjects. Beyond ESBL positive isolates, bla CTX-M group genes were the most common type (75.6%) and bla TEM (non-bla TEM-1 and non- bla TEM-2) were in the second place (25.6%). Among bla CTX-M genes, bla CTX-M-1 (55.3%) and bla CTX-M-15 (55.3%) were the most predominant types with equal prevalence. Some isolates were multi-enzyme producers. bla CIT and bla DHA genes were common AmpC type enzyme encoding genes found in AmpC-PE isolates. Most isolates produced both enzymes at the same time. The number of students in the classes was statistically associated with ESBL-PE intestinal carriage (p < 0.05). Moreover, 46 (65.7%), 3 (60%), 4 (100%), and 98 (39.8%) ESBL-, AmpC-, ESBL/AmpC, and non-ESBL/AmpC-PE isolates were multidrug-resistant, respectively. Overall, regardless of β-lactam antibiotics, 62% and 59.5% of isolates were resistant to co-trimoxazole and tetracycline, respectively. The majority of ESBL producing E. coli isolates (69.2%) belonged to phylogroup A. According to Enterobacterial repetitive intergenic consensus polymerase chain reaction, there was no clonal relatedness between isolates. This study showed a high rate of multi-resistant ESBL-PE intestinal carriage among healthy individuals in Iran.
Collapse
Affiliation(s)
- Nasrin Habibzadeh
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hadi Peeri Doghaheh
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Meysam Manouchehri Far
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hossein Alimohammadi Asl
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sohrab Iranpour
- Department of Community Medicine, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mohsen Arzanlou
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| |
Collapse
|
15
|
Zhong YM, Zhang XH, Ma Z, Liu WE. Prevalence of Escherichia coli ST1193 Causing Intracranial Infection in Changsha, China. Trop Med Infect Dis 2022; 7:tropicalmed7090217. [PMID: 36136628 PMCID: PMC9504535 DOI: 10.3390/tropicalmed7090217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
ST1193 is an emerging new virulent and resistant clone among Escherichia coli with a tendency to spread rapidly across the globe. However, the prevalence of intracranial infection-causing E. coli ST1193 is rarely reported. This study aimed at determining the prevalence of E. coli ST1193 isolates, causing intracranial infections in Changsha, central China. A total of 28 E. coli isolates were collected from the cerebrospinal fluid of patients with intracranial infection over a four-year period. All isolates were differentiated using multilocus sequence typing (MLST), and phylogenetic grouping, and tested for antibiotic resistance. MLST analysis showed 11 sequence types (ST) among the 28 E. coli isolates. The most prevalent ST was B2-ST1193 (28.6%, 8/28), followed by B2-ST131 (21.4%, 6/28) and F-ST648 (10.7%, 3/28). Of the eight ST1193 isolates, three carried CTX-M-55, and one carried CTX-M-27. All eight ST1193 isolates were resistant to Ciprofloxacin, showing gyrA1AB/parC4A mutations. Two ST1193 isolates carried the aac(6′)-Ib-cr gene. All ST1193 isolates were recovered from infants with meningitis, with a fatal outcome for one three-month-old infant. ST1193 has emerged as the predominant type of E. coli strain causing intracranial infections in Changsha, China. This study highlights the importance of implementing appropriate surveillance measures to prevent the spread of this emerging public health threat.
Collapse
Affiliation(s)
- Yi-Ming Zhong
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiao-He Zhang
- Faculty of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Zheng Ma
- Faculty of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Wen-En Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: ; Tel.: +86-731-84327437
| |
Collapse
|
16
|
Verma J, Jain D, Mallik D, Ghosh AS. Comparative insight into the roles of the non active-site residues E169 and N173 in imparting the beta-lactamase activity of CTX-M-15. FEMS Microbiol Lett 2022; 369:6530193. [PMID: 35175332 DOI: 10.1093/femsle/fnac018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/03/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
CTX-M-15 is a major extended-spectrum beta-lactamase disseminated throughout the globe. The roles of amino acids present in the active-site are widely studied though little is known about the role of the amino acids lying at the close proximity of the CTX-M-15 active-site. Here, by using site-directed mutagenesis we attempted to decipher the role of individual amino acids lying outside the active-site in imparting the beta-lactamase activity of CTX-M-15. Based on the earlier evidence, three amino acid residues namely, Glu169, Asp173 and Arg277 were substituted with alanine. The antibiotic susceptibility of E. coli cells harboring E169A and N173A substituted CTX-M-15 were enhanced by ∼ >32 fold for penicillins and ∼ 4-32 fold for cephalosporins, in comparison to CTX-M-15. However, cells carrying CTX-M-15_R277A did not show a significant difference in antibiotic susceptibility as compared to the wild-type. Further, the catalytic efficiency of the purified CTX-M-15_E169A and CTX-M-15_N173A were compromised when compared with the efficient beta-lactam hydrolysis of purified CTX-M-15. Moreover, the thermal stability of the mutated proteins CTX-M-15_E169A and CTX-M-15_N173A were reduced as compared to the wild type CTX-M-15. Therefore, we conclude that E169 and N173 are crucial non-active-site amino acids that are able to govern the CTX-M-15 activity.
Collapse
Affiliation(s)
- Jyoti Verma
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Diamond Jain
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Dhriti Mallik
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| |
Collapse
|
17
|
Outbreak of CTX-M-15 Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae ST394 in a French Intensive Care Unit Dedicated to COVID-19. Pathogens 2021; 10:pathogens10111426. [PMID: 34832582 PMCID: PMC8618658 DOI: 10.3390/pathogens10111426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
Infections caused by extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-KP) are constantly rising worldwide and are often reported as causative agent of outbreaks in intensive care units (ICUs). During the first wave of the COVID-19 pandemic, bacterial cross-transmission was thought unlikely to occur due to the reinforcement of hygiene measures and prevention control. However, we report here an ESBL-producing K. pneumoniae (ST394) isolate responsible for a nosocomial outbreak in an ICU dedicated to COVID-19 patients.
Collapse
|
18
|
Castanheira M, Simner PJ, Bradford PA. Extended-spectrum β-lactamases: an update on their characteristics, epidemiology and detection. JAC Antimicrob Resist 2021; 3:dlab092. [PMID: 34286272 PMCID: PMC8284625 DOI: 10.1093/jacamr/dlab092] [Citation(s) in RCA: 218] [Impact Index Per Article: 72.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Gram-negative pathogens are a major cause of resistance to expanded-spectrum β-lactam antibiotics. Since their discovery in the early 1980s, they have spread worldwide and an are now endemic in Enterobacterales isolated from both hospital-associated and community-acquired infections. As a result, they are a global public health concern. In the past, TEM- and SHV-type ESBLs were the predominant families of ESBLs. Today CTX-M-type enzymes are the most commonly found ESBL type with the CTX-M-15 variant dominating worldwide, followed in prevalence by CTX-M-14, and CTX-M-27 is emerging in certain parts of the world. The genes encoding ESBLs are often found on plasmids and harboured within transposons or insertion sequences, which has enabled their spread. In addition, the population of ESBL-producing Escherichia coli is dominated globally by a highly virulent and successful clone belonging to ST131. Today, there are many diagnostic tools available to the clinical microbiology laboratory and include both phenotypic and genotypic tests to detect β-lactamases. Unfortunately, when ESBLs are not identified in a timely manner, appropriate antimicrobial therapy is frequently delayed, resulting in poor clinical outcomes. Several analyses of clinical trials have shown mixed results with regards to whether a carbapenem must be used to treat serious infections caused by ESBLs or whether some of the older β-lactam-β-lactamase combinations such as piperacillin/tazobactam are appropriate. Some of the newer combinations such as ceftazidime/avibactam have demonstrated efficacy in patients. ESBL-producing Gram-negative pathogens will continue to be major contributor to antimicrobial resistance worldwide. It is essential that we remain vigilant about identifying them both in patient isolates and through surveillance studies.
Collapse
|
19
|
Selvakumar V, Kannan K, Panneerselvam A, Suresh M, Nooruddin T, Pal K, Elkodous MA, Nada HG, El-Bastawisy HS, Tolba MM, Noureldeen A, Darwish H, Fayad E, Khairy WA, Nasser HA, El-Sayyad GS. Molecular identification of extended spectrum β-lactamases (ESBLs)-producing strains in clinical specimens from Tiruchirappalli, India. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01886-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
20
|
Galani I, Karaiskos I, Giamarellou H. Multidrug-resistant Klebsiella pneumoniae: mechanisms of resistance including updated data for novel β-lactam-β-lactamase inhibitor combinations. Expert Rev Anti Infect Ther 2021; 19:1457-1468. [PMID: 33945387 DOI: 10.1080/14787210.2021.1924674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Multi-drug-resistant Klebsiella pneumoniae is currently one of the most pressing emerging issues in bacterial resistance. Treatment of K.pneumoniae infections is often problematic due to the lack of available therapeutic options, with a relevant impact in terms of morbidity, mortality and healthcare-associated costs. Soon after the launch of Ceftazidime-Avibactam, one of the approved new β-lactam/β-lactamase inhibitor combinations, reports of ceftazidime-avibactam-resistant strains developing resistance during treatment were published. Being a hospital-associated pathogen, K.pneumoniae is continuously exposed to multiple antibiotics resulting in constant selective pressure, which in turn leads to additional mutations that are positively selected.Areas covered: Herein the authors present the K.pneumoniae mechanisms of resistance to different antimicrobials, including updated data for ceftazidime-avibactam.Expert opinion: K.pneumoniae is a nosocomial pathogen commonly implicated in hospital outbreaks with a propensity for antimicrobial resistance toward mainstay β-lactam antibiotics and multiple other antibiotic classes. Following the development of drug resistance and understanding the mechanisms involved, we can improve the efficacy of current antimicrobials, by applying careful stewardship and rational use to preserve their potential utility. The knowledge on antibiotic resistance mechanisms should be used to inform the design of novel therapeutic agents that might not be subject to, or can circumvent, mechanisms of resistance.
Collapse
Affiliation(s)
- Irene Galani
- Medicine, Infectious Diseases Laboratory, 4thDepartment of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ilias Karaiskos
- 1st Department of Internal Medicine-Infectious Diseases, Hygeia General Hospital, Athens, Greece
| | - Helen Giamarellou
- 1 Department of Internal Medicine-Infectious Diseases, Hygeia General Hospital, Athens, Greece
| |
Collapse
|
21
|
Antioxidant Molecules as a Source of Mitigation of Antibiotic Resistance Gene Dissemination. Antimicrob Agents Chemother 2021; 65:AAC.02658-20. [PMID: 33753335 DOI: 10.1128/aac.02658-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/16/2021] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli is the most commonly identified human pathogen and a prominent microorganism of the gut microbiota. Acquired resistance to antibiotics in this species is driven mainly by horizontal gene transfer and plasmid acquisition. Currently, the main concern is the acquisition of extended-spectrum β-lactamases of the CTX-M type in E. coli, a worldwide-observed phenomenon. Plasmids encoding CTX-M enzymes have different scaffolds and conjugate at different frequencies. Here, we show that the conjugation rates of several plasmid types encoding broad-spectrum β-lactamases are increased when the E. coli donor strain is exposed to subinhibitory concentrations of diverse orally given antibiotics, including fluoroquinolones, such as ciprofloxacin and levofloxacin, but also trimethoprim and nitrofurantoin. This study provides insights into underlying mechanisms leading to increased plasmid conjugation frequency in relation to DNA synthesis inhibitor-type antibiotics, involving reactive oxygen species (ROS) production and probably increased expression of genes involved in the SOS response. Furthermore, we show that some antioxidant molecules currently approved for unrelated clinical uses, such as edaravone, p-coumaric acid, and N-acetylcysteine, may antagonize the ability of antibiotics to increase plasmid conjugation rates. These results suggest that several antioxidative molecules might be used in combination with these "inducer" antibiotics to mitigate the unwanted increased resistance plasmid dissemination.
Collapse
|
22
|
Yang YM, Osawa K, Kitagawa K, Hosoya S, Onishi R, Ishii A, Shirakawa T, Hirai I, Kuntaman K, Tanimoto H, Shigemura K, Fujisawa M. Differential effects of chromosome and plasmid bla CTX-M-15 genes on antibiotic susceptibilities in extended-spectrum beta-lactamase-producing Escherichia coli isolates from patients with urinary tract infection. Int J Urol 2021; 28:623-628. [PMID: 33811389 DOI: 10.1111/iju.14498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/28/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVES To compare antibiotic susceptibilities between chromosomal and plasmid blaCTX-M-15 locations in urinary tract infection-causing extended-spectrum β-lactamases-producing Escherichia coli blaCTX-M-15 isolated in Indonesia. METHODS A total of 84 strains identified as extended-spectrum β-lactamases-producing E. coli were isolated from patients with urinary tract infection in Indonesia in 2015. Antimicrobial susceptibility tests were performed on these strains using 18 antibiotics, and extended-spectrum β-lactamase bla genes were detected by polymerase chain reaction. Gene localization of blaCTX-M-15 -positive strains was confirmed by Southern blot hybridization, and epidemiological typing was conducted using multilocus sequence typing. RESULTS Of 54 strains harboring the blaCTX-M-15 gene, 27 showed localization on chromosome, 20 on plasmid, and seven on chromosome and plasmid. Most multilocus sequence typing sequence types of the 27 strains with chromosomal blaCTX-M-15 were ST405 (25.9%) and ST131 (22.2%) strains, whereas the 20 strains with plasmid-blaCTX-M-15 were mostly ST410 (55.0%). CONCLUSIONS Extended-spectrum β-lactamases-producing E. coli blaCTX-M-15 with plasmid genes show significantly higher resistant rates against piperacillin-tazobactam but lower resistant rates against chloramphenicol compared to chromosomal strains in Indonesian patients with urinary tract infection. Mechanistic investigations will be necessary to advance our knowledge of antimicrobial resistance in urinary tract infection.
Collapse
Affiliation(s)
- Young-Min Yang
- Division of Urology, Department of Organ Therapeutics, Faculty of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kayo Osawa
- Division of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan.,Department of Medical Technology, Kobe Tokiwa University, Kobe, Japan
| | - Koichi Kitagawa
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan.,Department of Advanced Medical Science, Kobe University Graduate School of Science, Technology and Innovation, Kobe, Japan
| | - Samiko Hosoya
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Reo Onishi
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Aya Ishii
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Toshiro Shirakawa
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan.,Department of Advanced Medical Science, Kobe University Graduate School of Science, Technology and Innovation, Kobe, Japan
| | - Itaru Hirai
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kuntaman Kuntaman
- Department of Microbiology, Faculty of Medicine, Airlangga University, Surabaya, Indonesia
| | - Hiroshi Tanimoto
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Katsumi Shigemura
- Division of Urology, Department of Organ Therapeutics, Faculty of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Masato Fujisawa
- Division of Urology, Department of Organ Therapeutics, Faculty of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| |
Collapse
|
23
|
Moremi N, Silago V, Mselewa EG, Chifwaguzi AP, Mirambo MM, Mushi MF, Matemba L, Seni J, Mshana SE. Extended-spectrum β-lactamase bla CTX-M-1 group in gram-negative bacteria colonizing patients admitted at Mazimbu hospital and Morogoro Regional hospital in Morogoro, Tanzania. BMC Res Notes 2021; 14:77. [PMID: 33640022 PMCID: PMC7913416 DOI: 10.1186/s13104-021-05495-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Objective The objective of this study was to determine the proportion of extended spectrum β-lactamase producing gram-negative bacteria (ESBL-GNB) colonizing patients admitted at Mazimbu hospital and Morogoro Regional hospital, in Morogoro, Tanzania. Rectal colonization with ESBL-GNB increases the risks of developing bacterial infections by extra-intestinal pathogenic ESBL-GNB. Results Of the 285 patients investigated, 123 (43.2%) carried ESBL-GNB in their intestines. Five of the 123 ESBL positive patients were colonized with two different bacteria, making a total of 128 ESBL producing isolates. Escherichia coli (n = 95, 74.2%) formed the majority of ESBL isolates. The proportion of CTX-M-1 group genes among ESBL isolates tested was 94.9% (93/98). History of antibiotic use (OR: 1.83, 95% CI: 1.1–3.2, P = 0.03), being on antibiotic treatment (OR: 2.61, 95% CI: 1.5–4.53, P = 0.001), duration of hospital stay (OR: 1.2, 95% CI: 1.1–1.3, P < 0.001) and history of previous admission (OR: 2.24, 95% CI: 1.2–4.1, P = 0.009) independently predicted ESBL-GNB carriage.
Collapse
Affiliation(s)
- Nyambura Moremi
- Quality Assurance & Training Centre, National Health Laboratory, P. O. Box 9083, Dar Es Salaam, Tanzania
| | - Vitus Silago
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences-Bugando, P. O. Box 1464, Mwanza, Tanzania.
| | - Erick G Mselewa
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences-Bugando, P. O. Box 1464, Mwanza, Tanzania
| | - Ashery P Chifwaguzi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences-Bugando, P. O. Box 1464, Mwanza, Tanzania
| | - Mariam M Mirambo
- Quality Assurance & Training Centre, National Health Laboratory, P. O. Box 9083, Dar Es Salaam, Tanzania
| | - Martha F Mushi
- Quality Assurance & Training Centre, National Health Laboratory, P. O. Box 9083, Dar Es Salaam, Tanzania
| | - Lucas Matemba
- National Institute for Medical Research, P. O. Box 805, Dodoma, Tanzania
| | - Jeremiah Seni
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences-Bugando, P. O. Box 1464, Mwanza, Tanzania
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences-Bugando, P. O. Box 1464, Mwanza, Tanzania
| |
Collapse
|
24
|
Tooke CL, Hinchliffe P, Bonomo RA, Schofield CJ, Mulholland AJ, Spencer J. Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl-enzyme conformational dynamics to extend antibiotic resistance. J Biol Chem 2021; 296:100126. [PMID: 33257320 PMCID: PMC7949053 DOI: 10.1074/jbc.ra120.016461] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/21/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Class A serine β-lactamases (SBLs) are key antibiotic resistance determinants in Gram-negative bacteria. SBLs neutralize β-lactams via a hydrolytically labile covalent acyl-enzyme intermediate. Klebsiella pneumoniae carbapenemase (KPC) is a widespread SBL that hydrolyzes carbapenems, the most potent β-lactams; known KPC variants differ in turnover of expanded-spectrum oxyimino-cephalosporins (ESOCs), for example, cefotaxime and ceftazidime. Here, we compare ESOC hydrolysis by the parent enzyme KPC-2 and its clinically observed double variant (P104R/V240G) KPC-4. Kinetic analyses show that KPC-2 hydrolyzes cefotaxime more efficiently than the bulkier ceftazidime, with improved ESOC turnover by KPC-4 resulting from enhanced turnover (kcat), rather than altered KM values. High-resolution crystal structures of ESOC acyl-enzyme complexes with deacylation-deficient (E166Q) KPC-2 and KPC-4 mutants show that ceftazidime acylation causes rearrangement of three loops; the Ω, 240, and 270 loops, which border the active site. However, these rearrangements are less pronounced in the KPC-4 than the KPC-2 ceftazidime acyl-enzyme and are not observed in the KPC-2:cefotaxime acyl-enzyme. Molecular dynamics simulations of KPC:ceftazidime acyl-enyzmes reveal that the deacylation general base E166, located on the Ω loop, adopts two distinct conformations in KPC-2, either pointing "in" or "out" of the active site; with only the "in" form compatible with deacylation. The "out" conformation was not sampled in the KPC-4 acyl-enzyme, indicating that efficient ESOC breakdown is dependent upon the ordering and conformation of the KPC Ω loop. The results explain how point mutations expand the activity spectrum of the clinically important KPC SBLs to include ESOCs through their effects on the conformational dynamics of the acyl-enzyme intermediate.
Collapse
Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA; Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, Ohio, USA
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom.
| |
Collapse
|
25
|
Tsang KK, Maguire F, Zubyk HL, Chou S, Edalatmand A, Wright GD, Beiko RG, McArthur AG. Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance. Microb Genom 2021; 7:mgen000500. [PMID: 33416461 PMCID: PMC8115898 DOI: 10.1099/mgen.0.000500] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 12/08/2020] [Indexed: 11/25/2022] Open
Abstract
Diagnosing antimicrobial resistance (AMR) in the clinic is based on empirical evidence and current gold standard laboratory phenotypic methods. Genotypic methods have the potential advantages of being faster and cheaper, and having improved mechanistic resolution over phenotypic methods. We generated and applied rule-based and logistic regression models to predict the AMR phenotype from Escherichia coli and Pseudomonas aeruginosa multidrug-resistant clinical isolate genomes. By inspecting and evaluating these models, we identified previously unknown β-lactamase substrate activities. In total, 22 unknown β-lactamase substrate activities were experimentally validated using targeted gene expression studies. Our results demonstrate that generating and analysing predictive models can help guide researchers to the mechanisms driving resistance and improve annotation of AMR genes and phenotypic prediction, and suggest that we cannot solely rely on curated knowledge to predict resistance phenotypes.
Collapse
Affiliation(s)
- Kara K. Tsang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Haley L. Zubyk
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Sommer Chou
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gerard D. Wright
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew G. McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
26
|
Hastak P, Fourment M, Darling AE, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP, Roy Chowdhury P. Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex. Emerg Microbes Infect 2020; 9:1780-1792. [PMID: 32686595 PMCID: PMC7473005 DOI: 10.1080/22221751.2020.1797541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/14/2020] [Indexed: 11/25/2022]
Abstract
The H30Rx subclade of Escherichia coli ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum β-lactams. Isolates EC233 and EC234, variants of ST131-H30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:H4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both harbour an IncFII_2 plasmid (pSPRC_Ec234-FII) that carries most of the resistance genes on an IS26 associated translocatable unit, two small plasmids and a novel IncI1 plasmid (pSPRC_Ec234-I). SNP-based phylogenetic analysis of the core genome of representatives within the ST131 clonal complex places both isolates in a subclade with three clinical Australian ST131-H30Rx clade-C isolates. A MrBayes phylogeny analysis of EC233 and EC234 indicates ST8196 share a most recent common ancestor with ST131-H30Rx strain EC70 isolated from the same hospital in 2013. Our study identified genomic hallmarks that define the ST131-H30Rx subclade in the ST8196 isolates and highlights a need for unbiased genomic surveillance approaches to identify novel high-risk MDR E. coli pathogens that impact healthcare facilities.
Collapse
Affiliation(s)
- Priyanka Hastak
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Mathieu Fourment
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Aaron E. Darling
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Garry S. A. Myers
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Steven P. Djordjevic
- The ithree institute, University of Technology Sydney, Ultimo, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Broadway, Australia
| | - Piklu Roy Chowdhury
- The ithree institute, University of Technology Sydney, Ultimo, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Broadway, Australia
| |
Collapse
|
27
|
Castanheira M, Doyle TB, Hubler C, Sader HS, Mendes RE. Ceftazidime-avibactam activity against a challenge set of carbapenem-resistant Enterobacterales: Ompk36 L3 alterations and β-lactamases with ceftazidime hydrolytic activity lead to elevated MIC values. Int J Antimicrob Agents 2020; 56:106011. [DOI: 10.1016/j.ijantimicag.2020.106011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/24/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022]
|
28
|
Ranaei MA, Shahraki-Zahedan S, Mohagheghi-Fard AH, Salimizand H, Ordoni R, Amini Y. Prevalence of the blaCTX-M and antibiotic resistance pattern among clinical isolates of Acinetobacter baumannii isolated from Zahedan, Southeast Iran. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
29
|
Livermore DM, Day M, Cleary P, Hopkins KL, Toleman MA, Wareham DW, Wiuff C, Doumith M, Woodford N. OXA-1 β-lactamase and non-susceptibility to penicillin/β-lactamase inhibitor combinations among ESBL-producing Escherichia coli. J Antimicrob Chemother 2020; 74:326-333. [PMID: 30388219 DOI: 10.1093/jac/dky453] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/08/2018] [Indexed: 02/06/2023] Open
Abstract
Background ESBL-producing Escherichia coli have expanded globally since the turn of the century and present a major public health issue. Their in vitro susceptibility to penicillin/inhibitor combinations is variable, and clinical use of these combinations against ESBL producers remains controversial. We hypothesized that this variability related to co-production of OXA-1 penicillinase. Methods During a national study we collected 293 ESBL-producing E. coli from bacteraemias, determined MICs by BSAC agar dilution, and undertook genomic sequencing with Illumina methodology. Results The collection was dominated by ST131 (n = 188 isolates, 64.2%) and blaCTX-M-15 (present in 229 isolates, 78.2%); over half the isolates (159/293, 54.3%) were ST131 with blaCTX-M-15. blaOXA-1 was found in 149 ESBL producers (50.9%) and blaTEM-1/191 in 137 (46.8%). Irrespective of whether all isolates were considered, or ST131 alone, there were strong associations (P < 0.001) between co-carriage of blaOXA-1 and reduced susceptibility to penicillin/inhibitor combinations, whereas there was no significant association with co-carriage of blaTEM-1/191. For piperacillin/tazobactam the modal MIC rose from 2 mg/L in the absence of blaOXA-1 to 8 or 16 mg/L in its presence; for co-amoxiclav the shift was smaller, from 4 or 8 to 16 mg/L, but crossed the breakpoint. blaOXA-1 was strongly associated with co-carriage also of aac(6')-Ib-cr, which compromises amikacin and tobramycin. Conclusions Co-carriage of OXA-1, a penicillinase with weak affinity for inhibitors, is a major correlate of resistance to piperacillin/tazobactam and co-amoxiclav in E. coli and is commonly associated with co-carriage of aac(6')-Ib-cr, which narrows aminoglycoside options.
Collapse
Affiliation(s)
- David M Livermore
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, PHE National Infection Service, London, UK.,Norwich Medical School, University of East Anglia, Norwich, UK
| | - Michaela Day
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, PHE National Infection Service, London, UK
| | | | - Katie L Hopkins
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, PHE National Infection Service, London, UK
| | | | - David W Wareham
- Blizard Institute, Queen Mary University of London, London, UK
| | | | - Michel Doumith
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, PHE National Infection Service, London, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, PHE National Infection Service, London, UK
| |
Collapse
|
30
|
Hastak P, Cummins ML, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP, Roy Chowdhury P. Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital. Microb Genom 2020; 6:e000371. [PMID: 32374251 PMCID: PMC7371115 DOI: 10.1099/mgen.0.000371] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 04/03/2020] [Indexed: 11/29/2022] Open
Abstract
This study sought to assess the genetic variability of Escherichia coli isolated from bloodstream infections (BSIs) presenting at Concord Hospital, Sydney during 2013-2016. Whole-genome sequencing was used to characterize 81 E. coli isolates sourced from community-onset (CO) and hospital-onset (HO) BSIs. The cohort comprised 64 CO and 17 HO isolates, including 35 multidrug-resistant (MDR) isolates exhibiting phenotypic resistance to three or more antibiotic classes. Phylogenetic analysis identified two major ancestral clades. One was genetically diverse with 25 isolates distributed in 16 different sequence types (STs) representing phylogroups A, B1, B2, C and F, while the other comprised phylogroup B2 isolates in subclades representing the ST131, ST73 and ST95 lineages. Forty-seven isolates contained a class 1 integron, of which 14 carried blaCTX -M-gene. Isolates with a class 1 integron carried more antibiotic resistance genes than isolates without an integron and, in most instances, resistance genes were localized within complex resistance loci (CRL). Resistance to fluoroquinolones could be attributed to point mutations in chromosomal parC and gyrB genes and, in addition, two isolates carried a plasmid-associated qnrB4 gene. Co-resistance to fluoroquinolone and broad-spectrum beta-lactam antibiotics was associated with ST131 (HO and CO), ST38 (HO), ST393 (CO), ST2003 (CO) and ST8196 (CO and HO), a novel ST identified in this study. Notably, 10/81 (12.3 %) isolates with ST95 (5 isolates), ST131 (2 isolates), ST88 (2 isolates) and a ST540 likely carry IncFII-IncFIB plasmid replicons with a full spectrum of virulence genes consistent with the carriage of ColV-like plasmids. Our data indicate that IncF plasmids play an important role in shaping virulence and resistance gene carriage in BSI E. coli in Australia.
Collapse
Affiliation(s)
- Priyanka Hastak
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Max L. Cummins
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
- Faculty of Medicine, University of Sydney, NSW Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
- Faculty of Medicine, University of Sydney, NSW Australia
| | - Garry S. A. Myers
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Steven P. Djordjevic
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Piklu Roy Chowdhury
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| |
Collapse
|
31
|
Mendes RE, Rhomberg PR, Lister T, Cotroneo N, Rubio A, Flamm RK. Evaluation of Antimicrobial Effects of a New Polymyxin Molecule (SPR741) When Tested in Combination with a Series of β-Lactam Agents Against a Challenge Set of Gram-Negative Pathogens. Microb Drug Resist 2020; 26:319-328. [DOI: 10.1089/mdr.2019.0198] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Troy Lister
- Spero Therapeutics Inc., Cambridge, Massachusetts
| | | | - Aileen Rubio
- Spero Therapeutics Inc., Cambridge, Massachusetts
| | | |
Collapse
|
32
|
Ranjith K, SaiAbhilash CR, Sai Prashanthi G, Padakandla SR, Sharma S, Shivaji S. Phylogenetic Grouping of Human Ocular Escherichia coli Based on Whole-Genome Sequence Analysis. Microorganisms 2020; 8:microorganisms8030422. [PMID: 32192112 PMCID: PMC7143957 DOI: 10.3390/microorganisms8030422] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/10/2020] [Accepted: 03/14/2020] [Indexed: 01/12/2023] Open
Abstract
Escherichia coli is a predominant bacterium in the intestinal tracts of animals. Phylogenetically, strains have been classified into seven phylogroups, A, B1, B2, C, D, E, and F. Pathogenic strains have been categorized into several pathotypes such as Enteropathogenic (EPEC), Enterotoxigenic (ETEC), Enteroinvasive (EIEC), Enteroaggregative (EAEC), Diffusely adherent (DAEC), Uropathogenic (UPEC), Shiga-toxin producing (STEC) or Enterohemorrhagic (EHEC) and Extra-intestinal pathogenic E. coli (ExPEC). E. coli also survives as a commensal on the ocular surface. However, under conditions of trauma and immune-compromised states, E. coli causes conjunctivitis, keratitis, endopthalmitis, dacyrocystitis, etc. The phylogenetic affiliation and the pathotype status of these ocular E. coli strains is not known. For this purpose, the whole-genome sequencing of the 10 ocular E. coli strains was accomplished. Based on whole-genome SNP variation, the ocular E. coli strains were assigned to phylogenetic groups A (two isolates), B2 (seven isolates), and C (one isolate). Furthermore, results indicated that ocular E. coli originated either from feces (enteropathogenic and enterotoxigenic), urine (uropathogenic), or from extra-intestinal sources (extra-intestinal pathogenic). A high concordance was observed between the presence of AMR (Antimicrobial Resistance) genes and antibiotic resistance in the ocular E. coli strains. Furthermore, several virulent genes (fimB to fimI, papB to papX, etc.) and prophages (Enterobacteria phage HK97, Enterobacteria phage P1, Escherichia phage D108 etc.) were unique to ocular E. coli. This is the first report on a whole-genome analysis of ocular E. coli strains.
Collapse
|
33
|
Abstract
β-Lactam antibiotics have been widely used as therapeutic agents for the past 70 years, resulting in emergence of an abundance of β-lactam-inactivating β-lactamases. Although penicillinases in Staphylococcus aureus challenged the initial uses of penicillin, β-lactamases are most important in Gram-negative bacteria, particularly in enteric and nonfermentative pathogens, where collectively they confer resistance to all β-lactam-containing antibiotics. Critical β-lactamases are those enzymes whose genes are encoded on mobile elements that are transferable among species. Major β-lactamase families include plasmid-mediated extended-spectrum β-lactamases (ESBLs), AmpC cephalosporinases, and carbapenemases now appearing globally, with geographic preferences for specific variants. CTX-M enzymes include the most common ESBLs that are prevalent in all areas of the world. In contrast, KPC serine carbapenemases are present more frequently in the Americas, the Mediterranean countries, and China, whereas NDM metallo-β-lactamases are more prevalent in the Indian subcontinent and Eastern Europe. As selective pressure from β-lactam use continues, multiple β-lactamases per organism are increasingly common, including pathogens carrying three different carbapenemase genes. These organisms may be spread throughout health care facilities as well as in the community, warranting close attention to increased infection control measures and stewardship of the β-lactam-containing drugs in an effort to control selection of even more deleterious pathogens.
Collapse
|
34
|
Maurya N, Jangra M, Tambat R, Nandanwar H. Alliance of Efflux Pumps with β-Lactamases in Multidrug-Resistant Klebsiella pneumoniae Isolates. Microb Drug Resist 2020; 25:1155-1163. [PMID: 31613200 PMCID: PMC6807647 DOI: 10.1089/mdr.2018.0414] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Nosocomial infections caused by Klebsiella pneumoniae are primarily characterized by a high prevalence of extended-spectrum β-lactamases (ESBL's) and a soaring pace of carbapenemase dissemination. Availability of limited antimicrobial agents as a therapeutic option for multidrug-resistant bacteria raises an alarming concern. This study aimed at the molecular characterization of multidrug-resistant K. pneumoniae clinical isolates and studied the role of efflux pumps in β-lactam resistance. Thirty-three isolates confirmed as ESBL-positive K. pneumoniae that harbored resistance genes to major classes of antibiotics. The results showed that CTX-M15 was the preeminent β-lactamase along with carbapenemases in ESBL-positive isolates. However, the efficacy of different antibiotics varied in the presence of lactamase inhibitors and efflux pump inhibitors (EPIs). Those showing increased efficacy of antibiotics with EPI were further explored for the expression of efflux pump genes and expressed a significantly different level of efflux pumps. We found that an isolate had higher expression of kpnF (SMR family) and kdeA (MATE family) pump genes relative to RND family pump genes. No mutations were observed in the genes for porins. Together, the findings suggest that β-lactamases are not the only single factor responsible for providing resistance against the existing β-lactam drugs. Resistance may increase many folds by simultaneous expression of RND family (the most prominent family in Gram-negative bacteria) and other efflux pump family.
Collapse
Affiliation(s)
- Navdezda Maurya
- Bioactive Screening & Clinical Microbiology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Manoj Jangra
- Bioactive Screening & Clinical Microbiology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Rushikesh Tambat
- Bioactive Screening & Clinical Microbiology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Hemraj Nandanwar
- Bioactive Screening & Clinical Microbiology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| |
Collapse
|
35
|
Peirano G, Pitout JDD. Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae: Update on Molecular Epidemiology and Treatment Options. Drugs 2020; 79:1529-1541. [PMID: 31407238 DOI: 10.1007/s40265-019-01180-3] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are a major global public health concern. Presently, Escherichia coli with CTX-Ms are the most common species associated with global ESBLs; CTX-M-15 is the most frequent CTX-M worldwide and is followed by CTX-M-14, which is often found in South-East Asia. Recent surveillance studies showed that CTX-M-27 is emerging in certain parts of the world especially in Japan and Europe. The population structure of ESBL-producing E. coli is dominated globally by an high-risk clone named ST131. Escherichia coli ST131 belongs to three clades (A, B, and C) and three different subclades (C1, C1-M27, and C2). Clade C1-M27 is associated with blaCTX-M-27, and C2 with blaCTX-M-15. Recent whole genome sequencing studies have shown that clade C has evolved from clade B in a stepwise fashion, resulting in one of the most influential global antimicrobial resistance clones that has emerged during the 2000's. Other important E. coli clones that have been detected among ESBL producers include ST405, ST38, ST648, ST410, and ST1193. The INCREMENT project has shown that ertapenem is as effective as other carbapenems for treating serious infections due to ESBL-producing Enterobacteriaceae. The results of the MERINO open-label randomized controlled study has provided clear evidence that piperacillin-tazobactam should be avoided for targeted therapy of blood-stream infections due to ESBL-producing E. coli and K. pneumoniae, regardless of the patient population, source of infection, bacterial species, and susceptibility result of piperacillin-tazobactam. Research is still warranted to define the optimal therapy of less severe infections due to ESBL-producing Enterobactericeae.
Collapse
Affiliation(s)
- Gisele Peirano
- Division of Microbiology, Alberta Public Laboratories, Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, AB, T2L 2K8, Canada.,Departments of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Johann D D Pitout
- Division of Microbiology, Alberta Public Laboratories, Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, AB, T2L 2K8, Canada. .,Departments of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada. .,Microbiology, Immunology and Infectious Diseases, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada. .,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
| |
Collapse
|
36
|
Montealegre MC, Talavera Rodríguez A, Roy S, Hossain MI, Islam MA, Lanza VF, Julian TR. High Genomic Diversity and Heterogenous Origins of Pathogenic and Antibiotic-Resistant Escherichia coli in Household Settings Represent a Challenge to Reducing Transmission in Low-Income Settings. mSphere 2020; 5:e00704-19. [PMID: 31941809 PMCID: PMC6968650 DOI: 10.1128/msphere.00704-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/14/2019] [Indexed: 11/25/2022] Open
Abstract
Escherichia coli is present in multiple hosts and environmental compartments as a normal inhabitant, temporary or persistent colonizer, and as a pathogen. Transmission of E. coli between hosts and with the environment is considered to occur more often in areas with poor sanitation. We performed whole-genome comparative analyses on 60 E. coli isolates from soils and fecal sources (cattle, chickens, and humans) in households in rural Bangladesh. Isolates from household soils were in multiple branches of the reconstructed phylogeny, intermixed with isolates from fecal sources. Pairwise differences between all strain pairs were large (minimum, 189 single nucleotide polymorphisms [SNPs]), suggesting high diversity and heterogeneous origins of the isolates. The presence of multiple virulence and antibiotic resistance genes is indicative of the risk that E. coli from soil and feces represent for the transmission of variants that pose potential harm to people. Analysis of the accessory genomes of the Bangladeshi E. coli relative to E. coli genomes available in NCBI identified a common pool of accessory genes shared among E. coli isolates in this geographic area. Together, these findings indicate that in rural Bangladesh, a high level of E. coli in soil is likely driven by contributions from multiple and diverse E. coli sources (human and animal) that share an accessory gene pool relatively unique to previously published E. coli genomes. Thus, interventions to reduce environmental pathogen or antimicrobial resistance transmission should adopt integrated One Health approaches that consider heterogeneous origins and high diversity to improve effectiveness and reduce prevalence and transmission.IMPORTANCEEscherichia coli is reported in high levels in household soil in low-income settings. When E. coli reaches a soil environment, different mechanisms, including survival, clonal expansion, and genetic exchange, have the potential to either maintain or generate E. coli variants with capabilities of causing harm to people. In this study, we used whole-genome sequencing to identify that E. coli isolates collected from rural Bangladeshi household soils, including pathogenic and antibiotic-resistant variants, are diverse and likely originated from multiple diverse sources. In addition, we observed specialization of the accessory genome of this Bangladeshi E. coli compared to E. coli genomes available in current sequence databases. Thus, to address the high level of pathogenic and antibiotic-resistant E. coli transmission in low-income settings, interventions should focus on addressing the heterogeneous origins and high diversity.
Collapse
Affiliation(s)
| | | | - Subarna Roy
- Food Microbiology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Muhammed Iqbal Hossain
- Food Microbiology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Mohammad Aminul Islam
- Food Microbiology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, USA
| | - Val F Lanza
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| |
Collapse
|
37
|
Abstract
Resistance to β-lactam antibiotics in Gram-negative bacteria is commonly associated with production of β-lactamases, including extended-spectrum β-lactamases (ESBLs) and carbapenemases belonging to different molecular classes: those with a catalytically active serine and those with at least one active-site Zn2+ to facilitate hydrolysis. To counteract the hydrolytic activity of these enzymes, combinations of a β-lactam with a β-lactamase inhibitor (BLI) have been clinically successful. However, some β-lactam-BLI combinations have lost their effectiveness against prevalent Gram-negative pathogens that produce ESBLs, carbapenemases or multiple β-lactamases in the same organism. In this Review, descriptions are provided for medically relevant β-lactamase families and various BLI combinations that have been developed or are under development. Recently approved inhibitor combinations include the inhibitors avibactam and vaborbactam of the diazabicyclooctanone and boronic acid inhibitor classes, respectively, as new scaffolds for future inhibitor design.
Collapse
|
38
|
CTX-M-33, a CTX-M-15 derivative conferring reduced susceptibility to carbapenems. Antimicrob Agents Chemother 2019:AAC.01515-19. [PMID: 31527021 DOI: 10.1128/aac.01515-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
CTX-M-type extended-spectrum ß-lactamases (ESBL) are widespread among Enterobacterales worldwide. The most common variant is CTX-M-15 hydrolyzing ceftazidime at high rate, but sparing carbapenems. We identified here CTX-M-33, a point mutant derivative of CTX-M-15 (Asp to Ser substitution at Ambler position 109), exhibiting a low carbapenemase activity. ß-Lactamase CTX-M-33 was identified in a Klebsiella pneumoniae isolate belonging to ST405, lacking the outer membrane protein OmpK36, that was resistant to broad-spectrum cephalosporins and ß-lactam/ß-lactamase inhibitor combinations, and displayed a decreased susceptibility to carbapenems. Comparative hydrolytic activity assays showed that CTX-M-33 hydrolyzed ceftazidime at a lower level than CTX-M-15, but significantly hydrolyzed meropenem. In addition, CTX-M-33 showed higher Mutant Prevention Concentration values and wider mutant selection window in presence of meropenem, in accordance with its observed hydrolytic properties. We identified here the very first CTX-M enzyme possessing a weak carbapenemase activity, that may correspond to an emerging phenomenon when considering its possibility to evolve from the widespread ESBL CTX-M-15.
Collapse
|
39
|
Lagoutte P, Lugari A, Elie C, Potisopon S, Donnat S, Mignon C, Mariano N, Troesch A, Werle B, Stadthagen G. Combination of ribosome display and next generation sequencing as a powerful method for identification of affibody binders against β-lactamase CTX-M15. N Biotechnol 2019; 50:60-69. [PMID: 30634000 DOI: 10.1016/j.nbt.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 01/15/2023]
Abstract
CTX-M15 is one of the most widespread, extended spectrum β-lactamases, a major determinant of antibiotic resistance representing urgent public health threats, among enterobacterial strains infecting humans and animals. Here we describe the selection of binders to CTX-M15 from a combinatorial affibody library displayed on ribosomes. Upon three increasingly selective ribosome display iterations, selected variants were identified by next generation sequencing (NGS). Nine affibody variants with high relative abundance bearing QRP and QLH amino acid motifs at residues 9-11 were produced and characterized in terms of stability, affinity and specificity. All affibodies were correctly folded, with affinities ranging from 0.04 to 2 μM towards CTX-M15, and successfully recognized CTX-M15 in bacterial lysates, culture supernatants and on whole bacteria. It was further demonstrated that the binding of affibody molecules to CTX-M15 modulated the enzyme's kinetic parameters. This work provides an approach using ribosome display coupled to NGS for the rapid generation of protein ligands of interest in diagnostic and research applications.
Collapse
Affiliation(s)
| | - Adrien Lugari
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Céline Elie
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | | | | | | | | | - Alain Troesch
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Bettina Werle
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France.
| | | |
Collapse
|
40
|
Gwon B, Yoon EJ, Kim D, Lee H, Shin JH, Shin JH, Shin KS, Kim YA, Uh Y, Kim HS, Kim YR, Jeong SH. Differences in Antimicrobial Resistance Phenotypes by the Group of CTX-M Extended-Spectrum β-Lactamase. ANNALS OF CLINICAL MICROBIOLOGY 2019. [DOI: 10.5145/acm.2019.22.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Bareum Gwon
- Department of Clinical Pathology, Sangji University College of Science, Wonju, Korea
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University School of Medicine, Gwangju, Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University Busan Paik Hospital, Busan, Korea
| | - Kyeong Seob Shin
- Department of Laboratory Medicine, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Young Ah Kim
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Young Uh
- Department of Laboratory Medicine, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Young Ree Kim
- Department of Laboratory Medicine, School of Medicine, Jeju National University, Jeju, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
41
|
Meredith HR, Andreani V, Ma HR, Lopatkin AJ, Lee AJ, Anderson DJ, Batt G, You L. Applying ecological resistance and resilience to dissect bacterial antibiotic responses. SCIENCE ADVANCES 2018; 4:eaau1873. [PMID: 30525104 PMCID: PMC6281428 DOI: 10.1126/sciadv.aau1873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/07/2018] [Indexed: 05/14/2023]
Abstract
An essential property of microbial communities is the ability to survive a disturbance. Survival can be achieved through resistance, the ability to absorb effects of a disturbance without a notable change, or resilience, the ability to recover after being perturbed by a disturbance. These concepts have long been applied to the analysis of ecological systems, although their interpretations are often subject to debate. Here, we show that this framework readily lends itself to the dissection of the bacterial response to antibiotic treatment, where both terms can be unambiguously defined. The ability to tolerate the antibiotic treatment in the short term corresponds to resistance, which primarily depends on traits associated with individual cells. In contrast, the ability to recover after being perturbed by an antibiotic corresponds to resilience, which primarily depends on traits associated with the population. This framework effectively reveals the phenotypic signatures of bacterial pathogens expressing extended-spectrum β-lactamases (ESBLs) when treated by a β-lactam antibiotic. Our analysis has implications for optimizing treatment of these pathogens using a combination of a β-lactam and a β-lactamase (Bla) inhibitor. In particular, our results underscore the need to dynamically optimize combination treatments based on the quantitative features of the bacterial response to the antibiotic or the Bla inhibitor.
Collapse
Affiliation(s)
| | - Virgile Andreani
- Inria Saclay–Île-de-France, Palaiseau, France
- Institut Pasteur, Paris, France
| | - Helena R. Ma
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Anna J. Lee
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Deverick J. Anderson
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Duke University School of Medicine, Durham, NC, USA
| | - Gregory Batt
- Inria Saclay–Île-de-France, Palaiseau, France
- Institut Pasteur, Paris, France
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| |
Collapse
|
42
|
Lee H, Yoon EJ, Kim D, Jeong SH, Won EJ, Shin JH, Kim SH, Shin JH, Shin KS, Kim YA, Uh Y, Yang JW, Kim IH, Park C, Lee KJ. Antimicrobial resistance of major clinical pathogens in South Korea, May 2016 to April 2017: first one-year report from Kor-GLASS. Euro Surveill 2018; 23:1800047. [PMID: 30352640 PMCID: PMC6199864 DOI: 10.2807/1560-7917.es.2018.23.42.1800047] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 05/31/2018] [Indexed: 12/26/2022] Open
Abstract
The Korean government established an antimicrobial resistance (AMR) surveillance system, compatible with the Global AMR Surveillance System (GLASS): Kor-GLASS. We describe results from the first year of operation of the Kor-GLASS from May 2016 to April 2017, comprising all non-duplicated clinical isolates of major pathogens from blood, urine, faeces and urethral and cervical swabs from six sentinel hospitals. Antimicrobial susceptibility tests were carried out by disk diffusion, Etest, broth microdilution and agar dilution methods. Among 67,803 blood cultures, 3,523 target pathogens were recovered. The predominant bacterial species were Escherichia coli (n = 1,536), Klebsiella pneumoniae (n = 597) and Staphylococcus aureus (n = 584). From 57,477 urine cultures, 6,394 E. coli and 1,097 K. pneumoniae were recovered. Bloodstream infections in inpatients per 10,000 patient-days (10TPD) were highest for cefotaxime-resistant E. coli with 2.1, followed by 1.6 for meticillin-resistant Sta. aureus, 1.1 for imipenem-resistant Acinetobacter baumannii, 0.8 for cefotaxime-resistant K. pneumoniae and 0.4 for vancomycin-resistant Enterococcus faecium. Urinary tract infections in inpatients were 7.7 and 2.1 per 10TPD for cefotaxime-resistant E. coli and K. pneumoniae, respectively. Kor-GLASS generated well-curated surveillance data devoid of collection bias or isolate duplication. A bacterial bank and a database for the collections are under development.
Collapse
Affiliation(s)
- Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
- These authors contributed equally to this study
| | - Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
- These authors contributed equally to this study
| | - Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eun Jeong Won
- Department of Laboratory Medicine, Chonnam National University School of Medicine, Gwangju, Republic of Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University School of Medicine, Gwangju, Republic of Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Chungbuk, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine and Paik Institute for Clinical Research, Inje University College of Medicine, Busan, Republic of Korea
| | - Kyeong Seob Shin
- Department of Laboratory Medicine, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
| | - Young Ah Kim
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Republic of Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Ji Woo Yang
- National Institute of Health, Centers of Disease Control and Prevention, Cheongju, Republic of Korea
| | - Il Hwan Kim
- National Institute of Health, Centers of Disease Control and Prevention, Cheongju, Republic of Korea
| | - Chan Park
- National Institute of Health, Centers of Disease Control and Prevention, Cheongju, Republic of Korea
| | - Kwang Jun Lee
- National Institute of Health, Centers of Disease Control and Prevention, Cheongju, Republic of Korea
| |
Collapse
|
43
|
Defining Substrate Specificity in the CTX-M Family: the Role of Asp240 in Ceftazidime Hydrolysis. Antimicrob Agents Chemother 2018; 62:AAC.00116-18. [PMID: 29632016 DOI: 10.1128/aac.00116-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/05/2018] [Indexed: 12/11/2022] Open
Abstract
The natural diversification of CTX-M β-lactamases led to the emergence of Asp240Gly variants in the clinic that confer reduced susceptibility to ceftazidime (CAZ). In this study, we compared the impact of this substitution on CAZ and ceftazidime-avibactam (CZA) MICs against isogenic Escherichia coli strains with different porin deficiencies. Our results show a noticeable increase in CAZ resistance in clones expressing Asp240Gly-harboring CTX-M when combined with OmpF porin deficiency. Kinetic analysis revealed that the kcat/Km for CAZ was 5- to 15-fold higher for all Asp240Gly variants but remained 200- to 725-fold lower than that for cefotaxime (CTX). In vitro selection of CAZ-resistant clones yielded nonsusceptible CTX-M producers (MIC of >16 μg/ml) only after overnight incubation; the addition of avibactam (AVI) decreased MICs to a susceptible range against these variants. In contrast, the use of CZA as a selective agent did not yield resistant clones. AVI inactivated both CTX-M-12 and CTX-M-96, with an apparent inhibition constant comparable to that of SHV-2 and 1,000-fold greater than that of PER-2 and CMY-2, and k2/K for CTX-M-12 was 24- and 35-fold higher than that for CTX-M-96 and CTX-M-15, respectively. Molecular modeling suggests that AVI interacts similarly with CTX-M-96 and CTX-M-15. We conclude that the impact of Asp240Gly in resistance may arise when other mechanisms are also present (i.e., OmpF deficiency). Additionally, CAZ selection could favor the emergence of CAZ-resistant subpopulations. These results define the role of Asp240 and the impact of the -Gly substitution and allow us to hypothesize that the use of CZA is an effective preventive strategy to delay the development of resistance in this family of extended-spectrum β-lactamases.
Collapse
|
44
|
Zorgani A, Almagatef A, Sufya N, Bashein A, Tubbal A. Detection of CTX-M-15 Among Uropathogenic Escherichia coli Isolated from Five Major Hospitals in Tripoli, Libya. Oman Med J 2017; 32:322-327. [PMID: 28804585 PMCID: PMC5534234 DOI: 10.5001/omj.2017.61] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVES Multidrug resistance (MDR) and emergence of extended-spectrum β-lactamases (ESBLs) among uropathogenic Escherichia coli have been reported worldwide, but there was no information on the detection of blaCTX-M-15 in major teaching hospitals in Libya. The aim of the study was to investigate the occurrence of CTX-M-15 β-lactamases producers isolated from five teaching hospitals in Tripoli, Libya. METHODS A total of 346 urine samples were collected from hospitalized patients in five teaching hospitals with a diagnosis of urinary tract infection (UTI). Phenotypic confirmation of ESBLs was confirmed by E-test strip; all ESBL-producing E. coli isolates were screened for the blaCTX-M-15 gene. RESULTS The distribution of ESBL-producing E. coli varied among the five hospitals. The highest proportion was identified in Tripoli Medical Centre (67.6%). There were extremely high proportions of isolates resistant to ceftriaxone, cefepime, and ceftazidime (93.0-100.0%) among ESBL producers compared to non-ESBL producers (2.2-4.7%). MDR was detected in 22.2% of isolates. The majority of isolates (85.9%) in which blaCTX-M-15 was identified were ESBL producers. There was a correlation (p < 0.001) between expression of CTX-M-15 and resistance to ceftazidime. CONCLUSIONS The isolation of MDR ESBL-producing uropathogens expressing the CTX-M-15 gene will limit the choices clinicians have to treat their patients with UTIs. Continued surveillance and implementation of efficient infection control measures are required.
Collapse
Affiliation(s)
- Abdulaziz Zorgani
- Medical Microbiology, Faculty of Medicine, University of Tripoli, Tripoli, Libya,Address correspondence and reprints request to: Abdulaziz Zorgani, Medical Microbiology, Faculty of Medicine, University of Tripoli, Tripoli, Libya. E-mail:
| | - Asma Almagatef
- Microbiology Department, Faculty of Pharmacy, University of Tripoli, Tripoli, Libya
| | - Najib Sufya
- Microbiology Department, Faculty of Pharmacy, University of Tripoli, Tripoli, Libya
| | - Abdulla Bashein
- Biochemistry Department, Faculty of Medicine, University of Tripoli, Tripoli, Libya
| | - Abdullatif Tubbal
- Department of Statistics, Faculty of Science, University of Tripoli, Tripoli, Libya
| |
Collapse
|
45
|
Lee K, Yong D, Jeong SH, Tulgaa K, Docquier JD, Rossolini GM, Chong Y. Genetic and biochemical characterisation of CTX-M-37 extended-spectrum β-lactamase from an Enterobacter cloacae clinical isolate from Mongolia. J Glob Antimicrob Resist 2017; 10:3-7. [PMID: 28587869 DOI: 10.1016/j.jgar.2017.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/06/2017] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVES The aims of this study were to determine the resistance level of a blaCTX-M-37-carrying Enterobacter cloacae isolate from Mongolia, to analyse kinetic parameters of the purified enzyme and to compare the genetic environment of the gene. METHODS Minimum inhibitory concentrations (MICs) were determined using the Clinical and Laboratory Standards Institute (CLSI) agar dilution method. Purified CTX-M-37 enzyme was used to determined kinetic parameters. The genetic environment of the blaCTX-M-37 gene in E. cloacae was compared with a Kluyvera cryocrescens isolate. RESULTS The E. cloacae isolate showed relatively low-level resistance to cefotaxime (MIC=16mg/L) compared with a CTX-M-3-producing strain (MIC=256mg/L), and CTX-M-37 had a lower kcat/Km value for cefotaxime (2.0μM-1s-1) compared with CTX-M-3 (3.5μM-1s-1), possibly due to Asn114Asp substitution. The blaCTX-M-37 gene in the E. cloacae isolate was carried on a conjugative plasmid and was associated with an ISEcp1 element containing the -35 and -10 putative promoter sequences TTGAAA and TACAAT, respectively, unlike in the K. cryocrescens isolate. CONCLUSIONS The CTX-M-37-producing E. cloacae isolate showed relatively low-level resistance to cefotaxime and the purified enzyme had lower kinetic parameters as the result of Asn114Asp substitution. Presence of an ISEcp1 element and putative promoters upstream of the blaCTX-M-37 gene in E. cloacae, but not in the K. cryocrescens isolate, indicated their roles in mobilisation and expression of the gene.
Collapse
Affiliation(s)
- Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Khosbayar Tulgaa
- Department of Molecular Biology and Genetics, Research Center of Antimicrobial Resistance, Health Sciences University of Mongolia, Zorig Str. 4, Ulaanbaatar, Mongolia
| | - Jean-Denis Docquier
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 1, I-53100 Siena, Italy
| | - Gian Maria Rossolini
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 1, I-53100 Siena, Italy
| | - Yunsop Chong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea.
| |
Collapse
|
46
|
Ayari K, Bourouis A, Chihi H, Mahrouki S, Naas T, Belhadj O. Dissemination and genetic support of broad-spectrum beta-lactam-resistant Escherichia coli strain isolated from two Tunisian hospitals during 2004-2012. Afr Health Sci 2017; 17:346-355. [PMID: 29062329 PMCID: PMC5637019 DOI: 10.4314/ahs.v17i2.8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The dissemination of extended-spectrum β-lactamase (ESBL)-producing bacteria presented a great concern worldwide. Gram-negative organisms such as Escherichia coli and Klebsiella pneumoniae are the most frequently isolated pathogens responsible for nosocomial infections. OBJECTIVES The aim of this study was to investigate and to follow the emergence of resistance and the characterization of Extended-Spectrum Beta-Lactamases (ESBL) among broad-spectrum beta-lactam-Escherichia coli clinical isolates recovered from the military hospital and Habib Thameur hospital in Tunisia. METHODS A total of 113 E.coli isolates obtained during the period 2004 through 2012 showed a significant degree of multi-resistance. Among these strains, the double-disk synergy test confirmed the ESBL phenotype in 46 isolates. These included 32(70%) strains from Hospital A and 14(30%) from Hospital B. RESULTS The ESBL was identified as CTX-M-15. The ESBL resistance was transferred by a 60 kb plasmid CTXM-15-producing isolates were unrelated according to the PFGE analysis and characterization of the regions surrounding the blaCTX-M-15 showed the ISEcp1 elements located in the upstream region of the bla gene and 20 of them truncated by IS26. CONCLUSION ESBL producing E. coli strains are a serious threat in the community in Tunisia and we should take into consideration any possible spread of such epidemiological resistance.
Collapse
Affiliation(s)
- Khaoula Ayari
- Laboratory of Biochemistry and technobiology, Faculty of Sciences of Tunis, University Tunis El Manar, 2092 El Manar II, Tunisia
| | - Amel Bourouis
- Laboratory of Biochemistry and technobiology, Faculty of Sciences of Tunis, University Tunis El Manar, 2092 El Manar II, Tunisia
| | - Hela Chihi
- Laboratory of Biochemistry and technobiology, Faculty of Sciences of Tunis, University Tunis El Manar, 2092 El Manar II, Tunisia
| | - Sihem Mahrouki
- Laboratory of Biochemistry and technobiology, Faculty of Sciences of Tunis, University Tunis El Manar, 2092 El Manar II, Tunisia
| | - Thierry Naas
- Bacteriology-Virology service. CHU Bicetre 78 rue du Général Leclerc, 94275 Le Kremlin-Bicetre
| | - Omrane Belhadj
- Laboratory of Biochemistry and technobiology, Faculty of Sciences of Tunis, University Tunis El Manar, 2092 El Manar II, Tunisia
| |
Collapse
|
47
|
CTX-M-15 and OXA-10 beta lactamases in multi drug resistant Pseudomonas aeruginosa : First report from Pakistan. Microb Pathog 2017; 105:240-244. [DOI: 10.1016/j.micpath.2017.02.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/23/2022]
|
48
|
Derakhshan S, Peerayeh SN, Bakhshi B. Genotyping and characterization of CTX-M-15 -producing Klebsiella pneumoniae isolated from an Iranian hospital. J Chemother 2017; 28:289-96. [PMID: 25734924 DOI: 10.1179/1973947815y.0000000002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The aims were to describe the genetic characterization of blaCTX-M-1 group gene in Klebsiella pneumoniae and to investigate the relationship between isolates by MLVA and PFGE. We analyzed 36 CTX-M group 1-ESBL producing K. pneumoniae. rmpA and wcaG virulence genes were identified by PCR. The genetic environment of blaCTX-M-1 was analyzed by PCR and sequencing. Plasmid replicons were determined using PCR-based replicon typing. The isolates were typed by MLVA and PFGE. All blaCTX-M-1 were blaCTX-M-15. The wcaG and rmpA were detected in 1 and 2 isolates, respectively. IncF were the most frequently detected replicons (63.88%). In all isolates, ISEcp1 was found upstream and orf477 downstream of blaCTX-M-15, IS26 was found in two isolates. MLVA identified 20 MLVA types, whereas PFGE identified 25 different profiles. The dissemination of CTX-M-15 in our isolates was due to the clonal spread of isolates and to the genetic transfer of mobile elements among unrelated strains.
Collapse
Affiliation(s)
- Safoura Derakhshan
- a Department of Bacteriology, Faculty of Medical Sciences , Tarbiat Modares University , Tehran , Iran
| | - Shahin Najar Peerayeh
- a Department of Bacteriology, Faculty of Medical Sciences , Tarbiat Modares University , Tehran , Iran
| | - Bita Bakhshi
- a Department of Bacteriology, Faculty of Medical Sciences , Tarbiat Modares University , Tehran , Iran
| |
Collapse
|
49
|
Tayh G, Ben Sallem R, Ben Yahia H, Gharsa H, Klibi N, Boudabous A, Ben Slama K. First Report of Extended-Spectrum β-Lactamases Among Clinical Isolates ofKlebsiella pneumoniaein Gaza Strip, Palestine. Microb Drug Resist 2017; 23:169-176. [DOI: 10.1089/mdr.2016.0089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Ghassan Tayh
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El Manar, Tunis, Tunisie
| | - Rym Ben Sallem
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El Manar, Tunis, Tunisie
| | - Houssem Ben Yahia
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El Manar, Tunis, Tunisie
| | - Haythem Gharsa
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El Manar, Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-Manar, Tunis, Tunisie
| | - Naouel Klibi
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El Manar, Tunis, Tunisie
| | - Abdellatif Boudabous
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El Manar, Tunis, Tunisie
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El Manar, Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-Manar, Tunis, Tunisie
| |
Collapse
|
50
|
Mohamed S, Marwa A, Hamada H, Amro H. Mutations in -lactamases detected in multidrug resistant gram negative bacteria isolated from community acquired urinary tract infections in Assiut, Egypt. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajmr2016.8150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|