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Zeng Z, Ye C, Hao J, Tang M, Xiao X, Jian C, Guo J, Ding Y, Liu J. Molecular epidemiological analysis of bla NDM-5-producing Klebsiella pneumoniae ST2407-K25 causing infection outbreaks in pediatric patients based on whole genome sequencing. Ann Clin Microbiol Antimicrob 2024; 23:91. [PMID: 39385261 PMCID: PMC11465861 DOI: 10.1186/s12941-024-00747-7] [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: 02/18/2023] [Accepted: 09/20/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Pediatric patients are vulnerable to the threat of carbapenem-resistant Klebsiella pneumoniae (CRKP) due to their limited immunity and few available antibiotics. Especially when these pathogens exhibit hypervirulent phenotypes, they are often associated with poor clinical outcomes. METHODS In this study, we investigated a CRKP outbreak in pediatric patients from 2019 to 2021 in a teaching hospital in China based on whole genome sequencing. We sequenced twenty-nine CRKP isolates isolated from unduplicated pediatric patients to understand their genetic relationships, virulence factors, resistance mechanisms, and transmission trajectories. Conjugation experiments were performed to evaluate the horizontal transfer ability of carbapenem resistance determinants in twenty-nine CRKP isolates. We then characterized these isolates for biofilm formation ability and serum resistance. Genetic relatedness, comparison of plasmids, and chromosomal locus variation of CRKP isolates were analyzed by bioinformatics. RESULTS All the isolates were carbapenemase-producers harbouring blaNDM-5. Among them, twenty-eight isolates belonged to the ST2407 group, with the consistent capsular serotype K25. The virulence-related factors: ureA, fim, ybtA, irp1/irp2, and mrkA were prevalent in these isolates. Additionally, most CRKP isolates showed moderately adherent biofilm formation. Although the ST2407 clonal group did not exhibit serum resistance, the heterogeneous level of serum resistance was related to the disruption of oqxR. Conjugation and WGS revealed that the blaNDM-5 carried by the twenty-eight CRKP ST2407 isolates was located on nonconjugative IncX3 plasmids associated with deleting the T4SS-encoding genes. Clonal transmission of CRKP ST2407 in pediatric patients was suggested by the phylogenetic tree. CONCLUSIONS Our study provides evidence of the clonal spread of blaNDM-5-producing K. pneumoniae in pediatric patients and the necessity for the T4SS system for horizontal transfer of the IncX3 plasmid carrying blaNDM-5. Additionally, the disruption of oqxR may have affected the serum resistance of CRKP. The results of this study emphasize the importance of continuously monitoring for CRKP infection in pediatric patients to prevent recurrent infections.
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Affiliation(s)
- Zhangrui Zeng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Caihong Ye
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jingchen Hao
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Miran Tang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xue Xiao
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chunxia Jian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinglan Guo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yinhuan Ding
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China.
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China.
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Prevalence, Antibiotics Resistance and Plasmid Profiling of Vibrio spp. Isolated from Cultured Shrimp in Peninsular Malaysia. Microorganisms 2022; 10:microorganisms10091851. [PMID: 36144453 PMCID: PMC9505939 DOI: 10.3390/microorganisms10091851] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
Vibrio is the most common bacterium associated with diseases in crustaceans. Outbreaks of vibriosis pose a serious threat to shrimp production. Therefore, antibiotics are commonly used as preventative and therapeutic measures. Unfortunately, improper use of antibiotics leads to antibiotic resistance. Nevertheless, information on the occurrence of Vibrio spp. and antibiotic use in shrimp, particularly in Malaysia, is minimal. This study aimed to provide information on the occurrence of Vibrio spp., its status of antibiotic resistance and the plasmid profiles of Vibrio spp. isolated from cultured shrimp in Peninsular Malaysia. Shrimp were sampled from seven farms that were located in different geographical regions of Peninsular Malaysia. According to the observations, 85% of the shrimp were healthy, whereas 15% were unhealthy. Subsequently, 225 presumptive Vibrio isolates were subjected to biochemical tests and molecular detection using the pyrH gene. The isolates were also tested for antibiotic susceptibility against 16 antibiotics and were subjected to plasmid profiling. Eventually, 13 different Vibrio spp. were successfully isolated and characterized using the pyrH gene. They were the following: V. parahaemolyticus (55%), V. communis (9%), V. campbellii (8%), V. owensii (7%), V. rotiferianus (5%), Vibrio spp. (4%), V. alginolyticus (3%), V. brasiliensis (2%), V. natriegens (2%), V. xuii (1%), V. harveyi (1%), V. hepatarius (0.4%) and P. damselae (3%). Antibiotic susceptibility profiles revealed that all isolates were resistant to penicillin G (100%), but susceptible to norfloxacin (96%). Furthermore, 16% of the isolates revealed MAR of less than 0.2, while 84% were greater than 0.2. A total of 125 isolates harbored plasmids with molecular weights between 1.0 and above 10 kb, detected among the resistant isolates. The resistant isolates were mediated by both chromosomal and plasmid factors. These findings support the use of surveillance data on the emerging patterns of antimicrobial-resistance and plasmid profiles of Vibrio spp. in shrimp farms. The findings from this study can be used to develop a better disease management strategy for shrimp farming.
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Ahmadi M, Ranjbar R, Behzadi P, Mohammadian T. Virulence factors, antibiotic resistance patterns, and molecular types of clinical isolates of Klebsiella Pneumoniae. Expert Rev Anti Infect Ther 2021; 20:463-472. [PMID: 34612762 DOI: 10.1080/14787210.2022.1990040] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Klebsiella pneumoniae is armed with a wide range of antibiotic resistance mechanisms that mostly challenge effective treatment. The aims of the current study were to identify the clinical strains of K. pneumoniaealso to determine their phenotypes and molecular characterization related to antimicrobial resistance and virulence genes. RESEARCH DESIGN AND METHODS In this investigation, clinical specimens from different hospitals located in Tehran, Iran, were collected during a nine-month period (December 2018 to August 2019). The K. pneumoniae strains were isolated and identified through standard microbial and biochemical assays. Additionally, disk diffusion, combined disk, Modified Hodge Test (MHT) and PCR were performed for antibiotic resistance and virulence gene analysis, respectively. RESULTS Eighty-four isolates of K. pneumoniae were subjected to the study. According to the combined disk and modified Hodge test results, 27 (52%) and 15 pathotypes (62.5%) out of resistant strains of isolated K. pneumoniae were detected as ESBL and KPC producers. The virulence genes of mrkD (94%) and magA (11%) were the highest and lowest among isolates, respectively. CONCLUSIONS The high prevalence of antibiotic resistance and virulence genes in conjunction with a significant relationship between the strains revealed a high pathogenic capacity of the isolated pathotypes of K. pneumoniae.
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Affiliation(s)
- Mitra Ahmadi
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Payam Behzadi
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Taher Mohammadian
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
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Ma DY, Huang HY, Zou H, Wu ML, Lin QX, Liu B, Huang SF. Carbapenem-Resistant Klebsiella aerogenes Clinical Isolates from a Teaching Hospital in Southwestern China: Detailed Molecular Epidemiology, Resistance Determinants, Risk Factors and Clinical Outcomes. Infect Drug Resist 2020; 13:577-585. [PMID: 32110068 PMCID: PMC7037117 DOI: 10.2147/idr.s235975] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/13/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose Little is known about the epidemiology and carbapenem-resistance determinants of carbapenem-resistant K. aerogenes (CRKA) isolated from a single medical center. The present study was initiated to characterize the molecular epidemiology and the carbapenem-resistance mechanisms of CRKA isolated during 2012–2018 from a teaching hospital in southwest China, and to investigate the risk factors and clinical outcomes of CRKA infections as well. Methods Pulsed-field gel electrophoresis (PFGE) was employed for epidemiological analysis. PCR amplification and DNA sequencing were used to examine the antibiotic-resistance determinants. Plasmids were extracted and characterized by PCR-based replicon typing and conjugation assays. In order to further investigate the risk factors and clinical outcomes of CRKA infections, a retrospective case–control study was also performed. Results PFGE analysis showed 32 different PFGE patterns among the 36 non-duplicated CRKA strains collected. Most of the isolates harbored multi-drug resistance (MDR) genes, including 2 (5.6%) carrying blaNDM-1, 1 (2.8%) harboring blaKPC-2, 13 (36.1%) carrying ESBL genes, 23 (63.9%) carrying ampC genes, 34 (94.4%) carrying quinolone resistance determinants (QRD) genes and 9 (25%) carrying aminoglycoside resistance determinants (ARD) genes. The outer membrane porins, OmpE35 and OmpE36, were, respectively, lost in 4 and 2 isolates. The efflux pump inhibition experiments were positive in 25 (69.4%) of the CRKA strains. Multivariate analysis indicated that hypo-albuminaemia, invasive procedures, and carbapenem exposure were independent risk factors for acquiring CRKA infections. Conclusion No clonality relationship was identified among most of the 36 CRKA isolates. The over-expression of ESBLs and AmpC coupled with the efflux pumps contributed to carbapenem resistance in K. aerogenes. Additionally, this is the first report of CRKA isolate co-harboring blaNDM-1, blaCTX-M-15, blaEBC, blaACC, acc (6ʹ)-Ib, armA, qnrD and loss of OmpE36 in China. Hypo-albuminaemia, invasive procedures and carbapenem exposure were associated with acquisition of CRKA infections.
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Affiliation(s)
- De-Yu Ma
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Han-Yu Huang
- Department of Radiology, Chongqing Health Center for Women and Children, Chongqing, People's Republic of China
| | - Hua Zou
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Meng-Lu Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Qiu-Xia Lin
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Bo Liu
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Shi-Feng Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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Li J, Huang ZY, Yu T, Tao XY, Hu YM, Wang HC, Zou MX. Isolation and characterization of a sequence type 25 carbapenem-resistant hypervirulent Klebsiella pneumoniae from the mid-south region of China. BMC Microbiol 2019; 19:219. [PMID: 31533609 PMCID: PMC6749629 DOI: 10.1186/s12866-019-1593-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/09/2019] [Indexed: 12/29/2022] Open
Abstract
Background The molecular characterization of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) isolates is not well studied. Our goal was to investigate the molecular epidemiology of CR-hvKP strains that were isolated from a Chinese hospital. Results All clinical carbapenem-resistant K. pneumoniae (CR-KP) isolates were collected and identified from patient samples between 2014 and 2017 from a Chinese hospital. The samples were subjected to screening for CR-hvKP by string test and the detection of the aerobactin gene. CR-hvKP isolates were further confirmed through neutrophil phagocytosis and a mice lethality assay. The CR-hvKP isolates were investigated for their capsular genotyping, virulence gene profiles, and the expression of carbapenemase genes by PCR and DNA sequencing. Multilocus sequence type (MLST) and pulsed-field gel electrophoresis (PFGE) were performed to exclude the homology of these isolates. Twenty strains were identified as CR-hvKP. These strains were resistant to imipenem and several other antibiotics, however, most were susceptible to amikacin. Notably, two isolates were not susceptible to tigecycline. Capsular polysaccharide synthesis genotyping revealed that 17 of the 20 CR-hvKP strains belonged to the K2 serotype, while the others belonged to serotypes other than K1, K2, K5, K20, and K57. The strains were found to be positive for 10 types of virulence genes and a variety of these genes coexisted in the same strain. Two carbapenemase genes were identified: blaKPC-2 (13/20) and blaNDM-1 (1/20). PFGE typing revealed eight clusters comprising isolates that belonged to MLST types ST25, ST11 and ST375, respectively. PFGE cluster A was identified as the main cluster, which included 11 isolates that belong to ST25 and mainly from ICU department. Conclusions Our findings suggest that hospital-acquired infections may contribute in part to the CR-hvKP strains identified in this study. It also suggests that ST25 CR-hvKP strain has a clonal distribution in our hospital. Therefore, effective surveillance and strict infection control strategies should be implemented to prevent outbreak by CR-hvKP strains in hospitals setting.
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Affiliation(s)
- Jun Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zi-Yan Huang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ting Yu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiao-Yan Tao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yong-Mei Hu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Hai-Chen Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ming-Xiang Zou
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Yang S, He T, Sun J, Sun S. Distinct Antimicrobial Resistance Profiling Of Clinically Important Aeromonas Spp. In Southwest China: A Seven-Year Surveillance Study. Infect Drug Resist 2019; 12:2971-2978. [PMID: 31571949 PMCID: PMC6756270 DOI: 10.2147/idr.s216926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/04/2019] [Indexed: 11/23/2022] Open
Abstract
Background Co-evolution of host and aeromonads has diversified their spectrums of diseases and antibiograms, while a paucity of data was concerning about this diversity in China. To fill this gap, this study was aimed to investigate and compare antimicrobial resistance (AMR) patterns of clinically important Aeromonas spp. from various clinical sources. Methods A multicenter retrospective surveillance study was conducted in Chongqing from 2011 to 2017. Data of strains were retrieved from the database of China Antimicrobial Resistance Surveillance System (CARSS). Whonet 5.6 and Graphpad Prism 6 Software were adopted to determine and compare distribution and AMR patterns. Results Among 1135 Aeromonas strains, Aeromonas hydrophila complex (65.6%, 745/1135) was the most predominant species, followed by Aeromonas veronii complex (16.7%, 190/1135) and Aeromonas caviae complex (15.3%, 174/1135). Sputum was the most frequent source of strains (27.7%), followed by wound (20.8%), bloodstream (10.8%) and urine (8.8%). Urinary strains demonstrated the highest resistance rates to ceftriaxone (65.6%), ceftazidime (52.1%), cefepime (38.3%), ciprofloxacin (47.7%) and trimethoprim-sulfamethoxazole (56.6%). Similar AMR pattern was observed in intestinal strains, with corresponding resistance rates of 29.4%, 28.9%, 22.2%, 27.3% and 45%, respectively. However, respiratory, bloodstream and skin strains exhibited resistance rates of less than 20% to most of the antimicrobials tested. In terms of species, approximately 30% of Aeromonas hydrophila complex and Aeromonas caviae complex strains were resistant to ceftriaxone and trimethoprim-sulfamethoxazole, while Aeromonas veronii complex strains harbored resistance rates of less than 20% to all tested antimicrobials. Although antibiograms of these species were distinct, they remained constant from 2011 to 2017. Conclusions Distinct AMR patterns between species and sources highlighted the predominance of Aeromonas hydrophila complex and high resistance of strains in urine and intestine to extended-spectrum cephalosporins, ciprofloxacin and trimethoprim-sulfamethoxazole in Southwest China. Temporally constant AMR patterns should not relax the vigilance of antimicrobial resistance in clinically important Aeromonas species.
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Affiliation(s)
- Shuangshuang Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Tong He
- Department of Laboratory Animal Medicine, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Jide Sun
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Shan Sun
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
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Liu H, Jia X, Zou H, Sun S, Li S, Wang Y, Xia Y. Detection and characterization of tigecycline heteroresistance in E. cloacae: clinical and microbiological findings. Emerg Microbes Infect 2019; 8:564-574. [PMID: 30945610 PMCID: PMC6455127 DOI: 10.1080/22221751.2019.1601031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tigecycline is regarded as a last-resort treatment for carbapenem-resistant Enterobacteriaceae (CRE), however, the emergence of tigecycline heteroresistance has posted the therapeutic challenge to combat this “nightmare bacteria”. The primary purpose of this study was to demonstrate the existence of tigecycline heteroresistance in carbapenem-resistant E. cloacae (TH-CRECL) and further to explore the epidemiological characteristics and underlying molecular mechanisms. Our study identified a relative low prevalence of carbapenem-resistant E. cloacae (CRECL) isolates, about 20.0% (28/140), as heteroresistance to tigecycline. Molecular genetic relatedness of these heteroresistant isolates were characterized epidemiologically sporadic. In addition, mechanistic analysis revealed that Phe-Arg-β-naphthylamide (PAβN) significantly reversed tigecycline MIC levels of resistant colonies in heteroresistant strains, as primarily related to the marked overproduction of efflux pump genes acrAB and oqxAB, as well as overexpression of transcriptional regulators (soxS and ramA). Moreover, logistic regression analysis showed that previous fluoroquinolone therapy was identified as the only potential independent risk factor for the acquisition of TH-CRECL. Most importantly, our data indicated that patients with TH-CRECL infection might lead to a remarkably prolonged hospital stay and deterioration in functional status. These findings emphasized the necessity of timely detection and intervention of patients infected with TH-CRECL.
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Affiliation(s)
- Hang Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Xiaojiong Jia
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Hua Zou
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Shan Sun
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Shuang Li
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Yonghong Wang
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Yun Xia
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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Molecular characterization, antimicrobial resistance and clinico-bioinformatics approaches to address the problem of extended-spectrum β-lactamase-producing Escherichia coli in western Saudi Arabia. Sci Rep 2018; 8:14847. [PMID: 30287889 PMCID: PMC6172265 DOI: 10.1038/s41598-018-33093-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/19/2018] [Indexed: 12/21/2022] Open
Abstract
The goal of this study was to genotypically characterize extended-spectrum β-lactamase-producing Escherichia coli isolates from the western region of Saudi Arabia and to identify active antibiotics against these isolates using phenotypic and molecular modeling. In total, 211 ESBL-producing E. coli isolates recovered from heterogeneous clinical specimens were identified by MALDI-TOF. Thirty-two sequence types (STs) were identified from a multilocus sequence typing (MLST) analysis of ESBL-producing E. coli, including a novel ST (ST8162). The most common ST in the Saudi and expatriate population was ST131, followed by ST38. All the isolates were multidrug resistant (MDR), and >95% of the isolates were resistant to third-generation (ceftriaxone and ceftazidime) and fourth-generation (cefepime) cephalosporins. The ESBL-positive E. coli isolates primarily harbored the blaCTX-M and blaTEM genes. No resistance was observed against the carbapenem antibiotic group. All the ESBL-producing E. coli isolates were observed to be susceptible to a ceftazidime/avibactam combination. Molecular interaction analyses of the docked complexes revealed the amino acid residues crucial for the binding of antibiotics and inhibitors to the modeled CTX-M-15 enzyme. Importantly, avibactam displayed the most robust interaction with CTX-M-15 among the tested inhibitors in the docked state (∆G = −6.6 kcal/mol). The binding free energy values for clavulanate, tazobactam and sulbactam were determined to be −5.7, −5.9 and −5.2 kcal/mol, respectively. Overall, the study concludes that ‘ceftazidime along with avibactam’ should be carefully used as a treatment option against only carbapenem-resistant MDR ESBL-producing E. coli in this region.
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Tian X, Sun S, Jia X, Zou H, Li S, Zhang L. Epidemiology of and risk factors for infection with extended-spectrum β-lactamase-producing carbapenem-resistant Enterobacteriaceae: results of a double case-control study. Infect Drug Resist 2018; 11:1339-1346. [PMID: 30214254 PMCID: PMC6120570 DOI: 10.2147/idr.s173456] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose Carbapenem-resistant Enterobacteriaceae (CRE) have been increasingly reported worldwide and pose a serious public threat, but the clinical significance of extended-spectrum β-lactamase (ESBL) production in CRE is not well established. Patients and methods A retrospective case–case–control study was conducted to identify the clinical characteristics of patients with ESBL-CRE. The susceptibility of isolates obtained from these patients was assessed. The detection of ESBL and carbapenemase-related genes was performed by PCR methods. Predictors of 30-day mortality in patients with ESBL-CRE infection were also identified in our study. Results A total of 149 patients with CRE infection caused by Enterobacter cloacae (n=74), Escherichia coli (n=38), and Klebsiella pneumoniae (n=37) were identified in Chongqing, Southwestern China, between January 2011 and December 2014. Of the 35 isolates detected with carbapenemase-related genes, 16 isolates had New Delhi metallo-β-lactamase (NDM), nine isolates had K. pneumoniae carbapenemase (KPC), seven isolates had imipenemase (IMP), and four isolates had oxacillinase (OXA)-1. One strain of enterobacter cloacae carried both NDM-1 and IMP-8 genes. ESBL isolates included the genes CTX-M (72/149), SHV (64/149), and TEM (54/149). All ESBL-CRE isolates exhibited ertapenem resistance, and the rate of cephalosporin resistance was relatively high in general. Independent risk factors for infection with ESBL-CRE included previous exposure to β-lactam antibiotics, transfer from another hospital, and some underlying diseases. In addition, solid tumors, hypoalbuminemia, and central venous catheters were independent predictors of mortality in patients with ESBL-CRE infection. Conclusion Physicians should understand the peculiar predictors for the identification of these organisms among high-risk patients.
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Affiliation(s)
- Xiaolang Tian
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China,
| | - Shan Sun
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China,
| | - Xiaojiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China,
| | - Hua Zou
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China,
| | - Shuang Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China,
| | - Liping Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China,
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Braun SD, Jamil B, Syed MA, Abbasi SA, Weiß D, Slickers P, Monecke S, Engelmann I, Ehricht R. Prevalence of carbapenemase-producing organisms at the Kidney Center of Rawalpindi (Pakistan) and evaluation of an advanced molecular microarray-based carbapenemase assay. Future Microbiol 2018; 13:1225-1246. [PMID: 29938540 DOI: 10.2217/fmb-2018-0082] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM A DNA microarray-based assay for the detection of antimicrobial resistance (AMR) genes was used to study carbapenemase-producing organisms at the Kidney Center of Rawalpindi, Pakistan. METHODS The evaluation of this assay was performed using 97 reference strains with confirmed AMR genes. Testing of 7857 clinical samples identified 425 Gram-negative bacteria out of which 82 appeared carbapenem resistant. These isolates were analyzed using VITEK-2 for phenotyping and the described AMR assay for genotyping. RESULTS The most prevalent carbapenemase gene was blaNDM and in 12 isolates we detected two carbapenemase genes (e.g., blaNDM/blaOXA-48). CONCLUSION Our prevalence data from Pakistan show that - as in other parts of the world - carbapenemase-producing organisms with different underlying resistance mechanisms are emerging, and this warrants intensified and constant surveillance.
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Affiliation(s)
- Sascha D Braun
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Bushra Jamil
- Department of Biogenetics, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Muhammad A Syed
- Department of Microbiology, University of Haripur, Haripur, Pakistan
| | - Shahid A Abbasi
- Department of Pathology, Al-Sayed Hospital (Pvt) Ltd, 1-Hill Park, Opp. Ayub Park, Jhelum Road, Rawalpindi, Pakistan
| | - Daniel Weiß
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Peter Slickers
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Stefan Monecke
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany.,Technische Universität Dresden, Medizinische Fakultät "Carl Gustav Carus", Dresden, Germany
| | - Ines Engelmann
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Ralf Ehricht
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
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Jia X, Dai W, Ma W, Yan J, He J, Li S, Li C, Yang S, Xu X, Sun S, Shi J, Zhang L. Carbapenem-Resistant E. cloacae in Southwest China: Molecular Analysis of Resistance and Risk Factors for Infections Caused by NDM-1-Producers. Front Microbiol 2018; 9:658. [PMID: 29670607 PMCID: PMC5893741 DOI: 10.3389/fmicb.2018.00658] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 03/21/2018] [Indexed: 11/16/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) has been considered a serious global threat, but carbapenem resistance remains relatively uncommon in E. cloacae, especially in China. The aim of this study was to characterize carbapenem-resistant E. cloacae (CR-ECL) isolates from 2012 to 2016 in Southwest China. Our study revealed that 20 (15.2%) of the 132 CR-ECL isolates obtained from patients were identified as NDM-1, with most isolates carrying the IncFIIA plasmids. Notably, we initially observed that the E. cloacae strain co-harbored NDM-1 and IMP-8 carbapenemases simultaneously. Analysis of the genetic environment of these two genes has revealed that the highly conserved regions (blaNDM-1-bleMBL-trpF-tat) are associated with the dissemination of NDM-1, while IS26, intI1, and tniC could be involved in the spread of IMP-8. Molecular epidemiology studies showed the nosocomial outbreak caused by NDM-1-producing E. cloacae ST88. Transferring from another hospital and previous carbapenem exposure were identified as independent risk factors for the acquisition of NDM-1-producing E. cloacae. These findings emphasize the need for intensive surveillance and precautions to monitor the further spread of NDM-1 in China.
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Affiliation(s)
- Xiaojiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Dai
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Weijia Ma
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jinrong Yan
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jianchun He
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuang Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Congya Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuangshuang Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiuyu Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shan Sun
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Shi
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Liping Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Yan J, Pu S, Jia X, Xu X, Yang S, Shi J, Sun S, Zhang L. Multidrug Resistance Mechanisms of Carbapenem Resistant Klebsiella pneumoniae Strains Isolated in Chongqing, China. Ann Lab Med 2018. [PMID: 28643488 PMCID: PMC5500738 DOI: 10.3343/alm.2017.37.5.398] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKP) is considered a serious global threat. However, little is known regarding the multidrug resistance (MDR) mechanisms of CRKP. This study investigated the phenotypes and MDR mechanisms of CRKP and identified their clonal characteristics. METHODS PCR and sequencing were utilized to identify antibiotic resistance determinants. Integron gene cassette arrays were determined by restriction fragment length polymorphism (RFLP) analysis. Multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used for epidemiological analysis. Plasmids were typed by using a PCR-based replicon typing and analyzed by conjugation and transformation assays. RESULTS Seventy-eight strains were identified as resistant to at least one carbapenem; these CRKP strains had a high prevalence rate (38.5%, 30/78) of carbapenemase producers. Additionally, most isolates harbored MDR genes, including Extended spectrum β-lactamases (ESBLs), AmpC, and quinolone and aminoglycoside resistance genes. Loss of porin genes was observed, and Class 1 integron was detected in 66.7% of the investigated isolates. PFGE and MLST results excluded the occurrence of clonal dissemination among these isolates. CONCLUSIONS A high prevalence of NDM-1 genes encoding carbapenem resistance determinants was demonstrated among the K. pneumoniae isolates. Importantly, this is the first report of bla(NDM-1) carriage in a K. pneumoniae ST1383 clone in China and of a MDR CRKP isolate co-harboring bla(NDM-1), bla(KPC-2), bla(CTX-M), bla(SHV), acc(6')-Ib, rmtB, qnrB, and acc(6')-Ib-cr.
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Affiliation(s)
- Jinrong Yan
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuli Pu
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojiong Jia
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiuyu Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuangshuang Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shan Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Liping Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Ben Helal R, Dziri R, Chedly M, Klibi N, Barguellil F, El Asli MS, Ben Moussa M. Occurrence and Characterization of Carbapenemase-Producing Enterobacteriaceae in a Tunisian Hospital. Microb Drug Resist 2018; 24:1361-1367. [PMID: 29596032 DOI: 10.1089/mdr.2018.0013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae have become of particular concern, since they were quickly disseminated in various areas in the world. The aim of the study was to investigate the prevalence of carbapenemase production among clinical isolates of Enterobacteriaceae recovered from the Military Hospital of Tunisia. Bacterial isolates (n = 125) were recovered from patients in diverse services from March 2014 to February 2016 and identified by Vitek II Compact®. The multiplex PCR for blaVIM, blaIMP, blaNDM, blaKPC, and blaOXA-48 with subsequent amplicon detection by reverse hybridization was performed with the Hyplex SuperBug ID test system (AmplexDiagnostics GmbH, Gars-Bahnhof, Germany). The 125 strains showed resistance to carbapenems of which 102 strains (81.6%) were carbapenemase-producing Enterobacteriaceae and were identified as Klebsiella pneumoniae (85.2%), Enterobacter cloacae (9.8%), Escherichia coli (2.9%), Providencia stuartii (0.9%) and Enterobacter aerogenes (0.9%). These strains were isolated mainly from blood, anal, and urine samples. Patients were mainly hospitalized in the intensive care units, surgery, and medical services. All strains were resistant to ertapenem (100%) and 55.8% showed resistance to imipenem. Carbapenemases genes detected in our study were as follows: blaOXA-48 (84 isolates), blaNDM-1 (8 isolates), blaOXA-48 + blaVIM (5 isolates), and blaOXA-48 + blaNDM-1 (5 isolates). Our research provides epidemiological data showing the quick spread of carbapenem-resistant bacteria in our region, which calls for new surveillance strategies and strict hygiene rules.
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Affiliation(s)
- Rania Ben Helal
- 1 Service of Microbiology, Military Hospital of Tunis HMPIT , Tunis, Tunisia
| | - Raoudha Dziri
- 2 Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El Manar , Tunis, Tunisia
| | - Meriem Chedly
- 1 Service of Microbiology, Military Hospital of Tunis HMPIT , Tunis, Tunisia
| | - Naouel Klibi
- 2 Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El Manar , Tunis, Tunisia
| | - Farouk Barguellil
- 1 Service of Microbiology, Military Hospital of Tunis HMPIT , Tunis, Tunisia
- 3 Department of Microbiology, Faculty of Pharmacy , University of Monastir, Monastir, Tunisia
| | - Mohamed Selim El Asli
- 1 Service of Microbiology, Military Hospital of Tunis HMPIT , Tunis, Tunisia
- 3 Department of Microbiology, Faculty of Pharmacy , University of Monastir, Monastir, Tunisia
| | - Mohamed Ben Moussa
- 1 Service of Microbiology, Military Hospital of Tunis HMPIT , Tunis, Tunisia
- 3 Department of Microbiology, Faculty of Pharmacy , University of Monastir, Monastir, Tunisia
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Vila J, Sáez-López E, Johnson JR, Römling U, Dobrindt U, Cantón R, Giske CG, Naas T, Carattoli A, Martínez-Medina M, Bosch J, Retamar P, Rodríguez-Baño J, Baquero F, Soto SM. Escherichia coli: an old friend with new tidings. FEMS Microbiol Rev 2018; 40:437-463. [PMID: 28201713 DOI: 10.1093/femsre/fuw005] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/23/2015] [Accepted: 02/04/2016] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli is one of the most-studied microorganisms worldwide but its characteristics are continually changing. Extraintestinal E. coli infections, such as urinary tract infections and neonatal sepsis, represent a huge public health problem. They are caused mainly by specialized extraintestinal pathogenic E. coli (ExPEC) strains that can innocuously colonize human hosts but can also cause disease upon entering a normally sterile body site. The virulence capability of such strains is determined by a combination of distinctive accessory traits, called virulence factors, in conjunction with their distinctive phylogenetic background. It is conceivable that by developing interventions against the most successful ExPEC lineages or their key virulence/colonization factors the associated burden of disease and health care costs could foreseeably be reduced in the future. On the other hand, one important problem worldwide is the increase of antimicrobial resistance shown by bacteria. As underscored in the last WHO global report, within a wide range of infectious agents including E. coli, antimicrobial resistance has reached an extremely worrisome situation that ‘threatens the achievements of modern medicine’. In the present review, an update of the knowledge about the pathogenicity, antimicrobial resistance and clinical aspects of this ‘old friend’ was presented.
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Affiliation(s)
- J Vila
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - E Sáez-López
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - J R Johnson
- VA Medical Center, Minneapolis, MN, USA, and University of Minnesota, Minneapolis, MN, USA
| | - U Römling
- Karolinska Institute, Stockholm, Sweden
| | - U Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - R Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - C G Giske
- Karolinska Institute, Stockholm, Sweden
| | - T Naas
- Hôpital de Bicêtre, Université Paris Sud, Le Kremlin-Bicêtre, France
| | - A Carattoli
- Department of infectious, parasitic and immune-mediated diseases, Istituto Superiore di Sanità, Rome, Italy
| | - M Martínez-Medina
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona, Spain
| | - J Bosch
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - P Retamar
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Departamento de Medicina, Universidad de Sevilla, Seville, Spain
| | - J Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Departamento de Medicina, Universidad de Sevilla, Seville, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - F Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - S M Soto
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
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15
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Sun K, Xu X, Yan J, Zhang L. Evaluation of Six Phenotypic Methods for the Detection of Carbapenemases in Gram-Negative Bacteria With Characterized Resistance Mechanisms. Ann Lab Med 2018; 37:305-312. [PMID: 28445009 PMCID: PMC5409027 DOI: 10.3343/alm.2017.37.4.305] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 12/16/2016] [Accepted: 02/22/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND We compared the performance of the modified Hodge test (MHT), Triton Hodge test (THT), Carba NP test (CNPt), simplified Carba NP test (CNPt-direct), blue-Carba NP test (BCT), and carbapenem inactivation method (CIM) for rapid and accurate carbapenemase detection. METHODS The methods were evaluated by using 256 gram-negative isolates, including 197 Enterobacteriaceae (79 Enterobacter spp., 74 Klebsiella spp., 33 Escherichia coli, 10 Citrobacter spp., and 1 Serratia marcescens), 51 Acinetobacter baumannii, and 8 Pseudomonas aeruginosa strains. The collection included 117 non-carbapenemase, 18 Klebsiella pneumoniae carbapenemases (KPC) producers, 46 New Delhi metallo-β-lactamases (NDM) producers, 11 imipenemases (IMP) producers, and 51 oxacillinases (OXA) producers, and 13 strains harboring two different carbapenemase genes. RESULTS The specificity of the THT (91.5%) was significantly lower than other methods, each of which had 100% specificity (P<0.003). This can be attributed to the false detection of Ampler class C β-lactamases (AmpC) carriers. The CNPt-direct and CIM yielded the highest sensitivities (P<0.003), which were comparable (92.8% vs 93.5%, P>0.999). Because of improved detection of NDM carriers, THT showed significantly higher sensitivity than the MHT (84.9% vs 75.5%, P<0.001). However, poor performances in detecting OXA still influenced the sensitivities of the CNPt (66.2%) and BCT (82.0%), as well as the MHT and THT. CONCLUSIONS CNPt-direct and CIM demonstrated the best performance for the efficient detection of carbapenemase among the six evaluated methods. Except the MHT and THT, the detection of carbapenemase-producing Enterobacteriaceae by all the other methods was acceptable, when the OXA-type carbapenemase was not prevalent.
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Affiliation(s)
- Kunling Sun
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiuyu Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jinrong Yan
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Liping Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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16
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Kallonen T, Brodrick HJ, Harris SR, Corander J, Brown NM, Martin V, Peacock SJ, Parkhill J. Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131. Genome Res 2017; 27:1437-1449. [PMID: 28720578 PMCID: PMC5538559 DOI: 10.1101/gr.216606.116] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 06/07/2017] [Indexed: 12/19/2022]
Abstract
Escherichia coli associated with urinary tract infections and bacteremia has been intensively investigated, including recent work focusing on the virulent, globally disseminated, multidrug-resistant lineage ST131. To contextualize ST131 within the broader E. coli population associated with disease, we used genomics to analyze a systematic 11-yr hospital-based survey of E. coli associated with bacteremia using isolates collected from across England by the British Society for Antimicrobial Chemotherapy and from the Cambridge University Hospitals NHS Foundation Trust. Population dynamics analysis of the most successful lineages identified the emergence of ST131 and ST69 and their establishment as two of the five most common lineages along with ST73, ST95, and ST12. The most frequently identified lineage was ST73. Compared to ST131, ST73 was susceptible to most antibiotics, indicating that multidrug resistance was not the dominant reason for prevalence of E. coli lineages in this population. Temporal phylogenetic analysis of the emergence of ST69 and ST131 identified differences in the dynamics of emergence and showed that expansion of ST131 in this population was not driven by sequential emergence of increasingly resistant subclades. We showed that over time, the E. coli population was only transiently disturbed by the introduction of new lineages before a new equilibrium was rapidly achieved. Together, these findings suggest that the frequency of E. coli lineages in invasive disease is driven by negative frequency-dependent selection occurring outside of the hospital, most probably in the commensal niche, and that drug resistance is not a primary determinant of success in this niche.
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Affiliation(s)
- Teemu Kallonen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Hayley J Brodrick
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jukka Corander
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
- Department of Biostatistics, University of Oslo, 0372 Oslo, Norway
| | - Nicholas M Brown
- Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom
| | - Veronique Martin
- British Society of Antimicrobial Chemotherapy, Birmingham B1 3NJ, United Kingdom
| | - Sharon J Peacock
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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Abdalhamid B, Elhadi N, Albunayan S, Alsamman K, Aljindan R. First description of methyltransferases in extensively drug-resistant Klebsiella pneumoniae isolates from Saudi Arabia. J Med Microbiol 2017. [DOI: 10.1099/jmm.0.000480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Baha Abdalhamid
- Department of Pathology and Laboratory Medicine, King Fahad Specialist Hospital, Dammam, P. O. Box 15215, Saudi Arabia
| | - Nasreldin Elhadi
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, University of Dammam, Al Khobar, P. O. Box 2435, Saudi Arabia
| | - Samar Albunayan
- Department of Pathology and Laboratory Medicine, King Fahad Specialist Hospital, Dammam, P. O. Box 15215, Saudi Arabia
| | - Khaldoon Alsamman
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, University of Dammam, Al Khobar, P. O. Box 2435, Saudi Arabia
| | - Reem Aljindan
- Department of Microbiology, College of Medicine, University of Dammam, Al Khobar, P. O. Box 2208, Saudi Arabia
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Epidemiological and clinical features for cefepime heteroresistant Escherichia coli infections in Southwest China. Eur J Clin Microbiol Infect Dis 2016; 35:571-8. [PMID: 26815433 DOI: 10.1007/s10096-015-2572-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/30/2015] [Indexed: 01/13/2023]
Abstract
Phenotypic heteroresistance (PHR) is common in a weight of microbes and plays an important role in the evolution of antibiotic resistance. However, PHR to cefepime (FEP-PHR) among invasive Escherichia coli (E. coli) has not been reported. This study aimed to report the characteristics of invasive E. coli with FEP-PHR traits and further to investigate the predisposing factors for its acquisition. A retrospective case-control study was conducted in a teaching hospital in Southwest China. A total of 319 successive and non-duplicate E. coli strains were isolated from blood and other sterile body fluids between July 2011 and August 2013. Among the seventy (70/319, 21.9 %) isolates harboring FEP-PHR traits, 30 (42.9 %) isolates were isolated from blood, 14 (20.0 %) isolates were isolated from bile, and 13 (18.6 %) isolates were isolated from drainage. FEP-PHR isolates were verified by population analysis profile (PAP) assays. Male gender, receipt of total parenteral nutrition, cephalosporins exposure, and production of extended spectrum betalactamases (ESBL) were independent risk factors for the acquisition of invasive E. coli with FEP-PHR traits. Pulsedfield gel electrophoresis (PFGE) revealed clonal diversity among the FEP-PHR isolates. The prevalence of heteroresistance to cefepime among invasive E. coli isolates merits great attention and heteroresistance may lead to the emergence of resistance strains. Therefore, systematical analysis of risk factors, careful interpretation of antibiotic susceptibility results and appropriate prescription of therapeutic strategy could help to prevent misreporting and therapeutic failure.
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Xu G, Jiang Y, An W, Wang H, Zhang X. Emergence of KPC-2-producing Escherichia coli isolates in an urban river in Harbin, China. World J Microbiol Biotechnol 2015; 31:1443-50. [PMID: 26149956 DOI: 10.1007/s11274-015-1897-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/03/2015] [Indexed: 01/18/2023]
Abstract
Three KPC-2-producing Escherichia coli (E1, E2, and E3) were recovered from water samples of an urban river in the city of Harbin, China. Antimicrobial susceptibility was determined by broth microdilution. Molecular characterization and genetic relatedness of the isolates were determined by polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and PCR-directed phylotyping. Plasmids were analyzed by conjugation, S1-PFGE, Southern blotting and PCR-based replicon typing (PBRT). The genetic environment of the bla KPC-2 gene was determined using PCR and sequencing. PCR analyses revealed that the E1 isolate carried the bla KPC-2, bla CMY-2, bla TEM-1, bla CTX-M-14, and qnrB2 genes and belonged to sequence type ST410, phylogenetic type A; the E2 isolate was assigned to ST131-B2 and carried the bla KPC-2, bla TEM-1, bla CTX-M-3, bla DHA-1, aac(6')-Ib-cr, and qnrS1 genes; while the E3 isolate was of ST648-D and possessed bla KPC-2, bla TEM-1, bla OXA-1, bla CTX-M-15, armA, and aac(6')-Ib-cr genes. PFGE demonstrated that each of the three KPC-2-producing E. coli isolates exhibited an individual XbaI patterns. The bla KPC-2 gene was located on plasmids of 60-140 kb with IncA/C, IncN, or non-typeable replicon types. The genetic environment of bla KPC-2 of the three strains was consistent with the genetic structure of bla KPC-2 on the plasmid pKP048.
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Affiliation(s)
- Guofeng Xu
- Department of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Road, Harbin, 150030, China
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Zhu L, Shen D, Zhou Q, Li Z, Fang X, Li QZ. A locked nucleic acid (LNA)-based real-time PCR assay for the rapid detection of multiple bacterial antibiotic resistance genes directly from positive blood culture. PLoS One 2015; 10:e0120464. [PMID: 25775001 PMCID: PMC4361058 DOI: 10.1371/journal.pone.0120464] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
Bacterial strains resistant to various antibiotic drugs are frequently encountered in clinical infections, and the rapid identification of drug-resistant strains is highly essential for clinical treatment. We developed a locked nucleic acid (LNA)-based quantitative real-time PCR (LNA-qPCR) method for the rapid detection of 13 antibiotic resistance genes and successfully used it to distinguish drug-resistant bacterial strains from positive blood culture samples. A sequence-specific primer-probe set was designed, and the specificity of the assays was assessed using 27 ATCC bacterial strains and 77 negative blood culture samples. No cross-reaction was identified among bacterial strains and in negative samples, indicating 100% specificity. The sensitivity of the assays was determined by spiking each bacterial strain into negative blood samples, and the detection limit was 1–10 colony forming units (CFU) per reaction. The LNA-qPCR assays were first applied to 72 clinical bacterial isolates for the identification of known drug resistance genes, and the results were verified by the direct sequencing of PCR products. Finally, the LNA-qPCR assays were used for the detection in 47 positive blood culture samples, 19 of which (40.4%) were positive for antibiotic resistance genes, showing 91.5% consistency with phenotypic susceptibility results. In conclusion, LNA-qPCR is a reliable method for the rapid detection of bacterial antibiotic resistance genes and can be used as a supplement to phenotypic susceptibility testing for the early detection of antimicrobial resistance to allow the selection of appropriate antimicrobial treatment and to prevent the spread of resistant isolates.
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Affiliation(s)
- Lingxiang Zhu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Department of Immunology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Dingxia Shen
- Department of Clinical Microbiology, General Hospital of People’s Liberation Army, Beijing, China
| | - Qiming Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zexia Li
- Department of Immunology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Quan-Zhen Li
- Department of Immunology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- * E-mail:
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Zhang F, Zhu D, Xie L, Guo X, Ni Y, Sun J. Molecular epidemiology of carbapenemase-producing Escherichia coli and the prevalence of ST131 subclone H30 in Shanghai, China. Eur J Clin Microbiol Infect Dis 2015; 34:1263-9. [PMID: 25759112 DOI: 10.1007/s10096-015-2356-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/23/2015] [Indexed: 11/29/2022]
Abstract
The molecular characteristics and epidemiology of carbapenemase-producing Escherichia coli (CPEC) isolates from Shanghai, China, were investigated using 21 imipenem-resistant E. coli isolates obtained from a Shanghai teaching hospital from 2011 to 2014. The presence of bla KPC, bla IMP, bla VIM, bla OXA-48, and bla NDM was assessed by polymerase chain reaction (PCR) amplification and sequencing. CPEC isolates were characterized by the Etest®, multilocus sequence typing (MLST), and pulse-field gel electrophoresis (PFGE). Plasmids carrying resistance genes were analyzed by conjugation experiments, replicon typing, plasmid MLST (pMLST), S1 nuclease PFGE (S1-PFGE), and Southern hybridization. The genetic environment of the resistance genes was determined by PCR and sequencing. Among the 21 E. coli isolates, 16 produced carbapenemases; of these, ten isolates transferred carbapenemase-encoding plasmids to recipient bacteria. Nine of the 16 isolates were clonally related, and their PFGE patterns were designated type A. ST131 was the predominant sequence type (11 isolates, 68.8 %); the H30 subclone comprised 81.8 % of the ST131 strains. In all three isolates, bla IMP-4 was located on 50-kb IncN plasmids. All but two bla KPC-2 genes were carried on IncF plasmids of various sizes. Hence, both clone-spread and horizontal transfer mediated the dissemination of carbapenemase-producing genes in the Shanghai isolates.
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Affiliation(s)
- F Zhang
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin No. 2 Road, Shanghai, 200025, China
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Shi H, Sun F, Chen J, Ou Q, Feng W, Yong X, Xia P. Epidemiology of CTX-M-type extended-spectrum beta-lactamase (ESBL)-producing nosocomial -Escherichia coli infection in China. Ann Clin Microbiol Antimicrob 2015; 14:4. [PMID: 25591816 PMCID: PMC4299296 DOI: 10.1186/s12941-015-0063-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/08/2015] [Indexed: 12/22/2022] Open
Abstract
Background Escherichia coli is one of the most common clinical pathogens causing nosocomial infection. The widespread cefotaxime-beta lactamases (CTX) has increased the multidrug resistance (MDR) of E. coli and has brought great trouble to the doctor treating the infection. Methods ESBL-positive E. coli isolates were collected from different hospitals in different areas and the minimal inhibitory concentration (MIC) was analyzed by the agar dilution method. The resistance gene types were detected using polymerase chain reaction (PCR) and the sequence types were determined by multilocus sequence typing (MLST). Results We found that the blaCTX-M-1 group and the blaCTX-M-9 group were the main CTX-M gene types, with many kinds of MLST gene types. Except for TEM with high isolate, SHV, OXA and VEB were relatively rare, while no PER and GES was detected. Most strains may have other resistance mechanisms, and the ESBL positive strains have high resistance not only to cephalosporins but also to other kinds of antibiotics. Conclusion The study provides wide epidemiological data and enables more effective infection control and treatment plans.
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Affiliation(s)
- Huiqing Shi
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China. .,Department of Clinical Pharmacy, General Hospital of Chengdu Military Region, Chengdu, Sichuan Province, 610083, China.
| | - Fengjun Sun
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China.
| | - Jianhong Chen
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China.
| | - Qianyi Ou
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China.
| | - Wei Feng
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China.
| | - Xiaolan Yong
- Department of Clinical Pharmacy, General Hospital of Chengdu Military Region, Chengdu, Sichuan Province, 610083, China.
| | - Peiyuan Xia
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China.
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Impact of carbapenem heteroresistance among clinical isolates of invasive Escherichia coli in Chongqing, southwestern China. Clin Microbiol Infect 2014; 21:469.e1-10. [PMID: 25649300 DOI: 10.1016/j.cmi.2014.12.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/09/2014] [Accepted: 12/13/2014] [Indexed: 11/21/2022]
Abstract
Although heteroresistance is common in a wide range of microorganisms, carbapenem heteroresistance among invasive Escherichia coli infections has not been reported. The objective of this study was to evaluate the clinical significance of carbapenem heteroresistance and to identify risk factors for its acquisition. A case-control study was conducted at a 3200-bed teaching hospital in Chongqing, southwestern China. Successive and non-duplicate nosocomial E. coli isolates (n = 332) were obtained from July 2011 to June 2013. Bloodstream isolates made up 50.6% of the strains collected. The rates of heteroresistance were 25.0% to imipenem, 17.2% to ertapenem, and 3.9% to meropenem. The population analysis profile revealed the presence of subpopulations with higher carbapenem resistance, showing MICs ranging from 2.0-128.0mg/L. Male gender, invasive intervention, antibiotic use and bacterial extended-spectrum β-lactamase (ESBL) production contributed to invasive infections by carbapenem-heteroresistant E. coli (CHEC). The production of ESBL was identified as the common independent risk factor for heteroresistance to both ertapenem and imipenem. Pulsed-field gel electrophoresis revealed clonal diversity among the CHEC isolates. Most importantly, characterization of two successive E. coli strains isolated from the same patient indicated that carbapenem resistance evolved from heteroresistance. In conclusion, the high prevalence of heteroresistance to carbapenem among invasive E. coli merits great attention. Routine detection of ESBLs and the prudent use of imipenem and ertapenem are advocated. The early targeted intervention should be formulated to reduce CHEC infection and carbapenem resistance of E. coli.
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