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Qamar MU, Rizwan M, Uppal R, Khan AA, Saeed U, Ahmad K, Iqbal MJ, Ali Z, Suleman M. Antimicrobial susceptibility and clinical characteristics of multidrug-resistant polymicrobial infections in Pakistan, a retrospective study 2019-2021. Future Microbiol 2023; 18:1265-1277. [PMID: 37882773 DOI: 10.2217/fmb-2023-0110] [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: 05/12/2023] [Accepted: 07/24/2023] [Indexed: 10/27/2023] Open
Abstract
Background: We determined the prevalence of antimicrobial resistance (AMR) in polymicrobial pathogens in Pakistan. Methods: A total of 70,518 clinical samples were collected aseptically and confirmation of isolates and antibiogram were performed by the VITEK 2 system. Results: Of 70,518 samples, 441 (0.62%) were polymicrobial samples, with 882 (1.2%) polymicrobial pathogens with 689 (78.1%) Gram-negative rods (GNRs), 166 (18.8%) Gram-positive cocci and 27 (3.1%) Candida albicans. Among GNRs, 28.8% were Escherichia coli and 25.9% were Klebsiella pneumoniae. Majority, 15.1% of Pseudomonas aeruginosa and K. pneumoniae were found in combination. 30.1% of isolates were ESBL producers, 9.7% carbapenem-resistant organisms, 35.5% MRSA and 6.0% VRE. 100% of E. coli were resistant to ampicillin and 98% of K. pneumoniae were resistant to piperacillin. Conclusion: A high prevalence of AMR in polymicrobial pathogens was observed.
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Affiliation(s)
- Muhammad Usman Qamar
- Institute of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
| | - Muhammad Rizwan
- Department of Pathology, Islamabad Diagnostic Center, Faisalabad, 38000, Pakistan
| | - Rizwan Uppal
- Department of Pathology, Islamabad Diagnostic Center, Islamabad, Pakistan
| | - Aftab Ahmad Khan
- Department of Pathology, Islamabad Diagnostic Center, Islamabad, Pakistan
| | - Umar Saeed
- Department of Pathology, Islamabad Diagnostic Center, Islamabad, Pakistan
- Department of Clinical and Biomedical Research Center, Foundation University School of Health Sciences, Foundation University Islamabad, Pakistan
| | - Khurshid Ahmad
- Department of Pathology, Islamabad Diagnostic Center, Islamabad, Pakistan
| | | | - Zuhaib Ali
- Department of Pathology, Islamabad Diagnostic Center, Islamabad, Pakistan
| | - Muhammad Suleman
- Department of Pathology, Islamabad Diagnostic Center, Islamabad, Pakistan
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Ibik YE, Ejder N, Sevim E, Rakici E, Tanriverdi ES, Copur Cicek A. Evaluating molecular epidemiology of carbapenem non-susceptible Klebsiella pneumoniae isolates with MLST, MALDI-TOF MS, PFGE. Ann Clin Microbiol Antimicrob 2023; 22:93. [PMID: 37891628 PMCID: PMC10612262 DOI: 10.1186/s12941-023-00640-9] [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: 02/27/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND This study aimed to evaluate antibiotic resistance genes and virulence genes and the clonal relationship of the carbapenem-nonsusceptible Klebsiella pneumoniae strains by molecular methods which are isolated from various clinical specimens from patients treated in tertiary care hospital in Turkey. METHODS Identification of 32 carbapenem non-susceptible K. pneumoniae were determined by VITEK-2 (BioMérieux, France) automated system. Thirteen colistin-resistant strains were tested with the broth microdilution method. Various antibiotic resistance genes and virulence genes frequently seen in carbapenem-resistant strains were screened by PCR. Immunochromatographic tests used in the rapid diagnosis of carbapenemases were compared with PCR results. In addition, PFGE, MLST and MALDI-TOF MS methods were used to determine the clonal relationship among these strains. RESULTS PCR demonstrated that 31 of the strains carried at least one of the carbapenemase genes. In one strain, the coexistence of blaOXA-48+NDM was shown. The most common resistance genes were determined as blaSHV (84.3%), blaCTX-M-1 (46.8%), blaOXA-48 (40.6%), blaKPC (40.6%), blaTEM (31.2%), blaNDM (18.8%) respectively. Among the virulence genes; magA (68.7%) was the most common, followed by kpn (59.3%) and K2 (9.3%). Immunochromatographic tests were found to be 100% compatible with PCR results. All colistin-resistant isolates were also found to be resistant by colistin broth microdilution. In PFGE analysis, 25 different genotypes were determined and clustering isolates were collected in 5 different clusters and the clustering rate was 35.4%. In MLST analysis, ST101 type was determined as the most common ST type with a rate of 29%. ST101 is followed by ST16, ST307, ST14, ST147, ST309, ST377, ST395 and ST2096, respectively. The compatibility rate between MALDI-TOF MS and VITEK-2 was found 94.3%, in bacterial identification. In MALDI-TOF MS typing, the maximum similarity between the strains was less than 70% and clustering not shown. CONCLUSION In addition to OXA-48, which is endemic in our country, it has been determined that KPC, which is more common in the world, is becoming increasingly common in our region. ST101 type was determined as the most common type between the strains. To the best of our knowledge, this is the first study that compares these three methods in our country. There may be differences between bacterial identifications made with VITEK-2 and MALDI-TOF MS. In this study, it was observed that MALDI-TOF MS analyses were not compatible with the typing of strains according to PFGE and MLST analysis results.
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Affiliation(s)
- Yunus Emre Ibik
- Microbiology Laboratory, Ordu University Training and Research Hospital, Ordu, 52000, Turkey.
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey.
| | - Nebahat Ejder
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Elif Sevim
- Department of Medical Biology, Faculty of Medicine, Ahi Evran University, Kırşehir, Turkey
| | - Erva Rakici
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | | | - Aysegül Copur Cicek
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
- Department of Medical Microbiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey
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Zhang X, Zhu Y, Gao Y, Li W, Wang Y, Li Y. Evaluation and analysis of multidrug resistance- and hypervirulence-associated genes in carbapenem-resistant Pseudomonas aeruginosa strains among children in an area of China for five consecutive years. Front Microbiol 2023; 14:1280012. [PMID: 37901827 PMCID: PMC10602738 DOI: 10.3389/fmicb.2023.1280012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a growing threat. It is urgent to investigate the multidrug resistance and high virulence of CRPA to provide a basis for infection control and rational use of antibiotics. Methods A retrospective study of 56 nonduplicated CRPA isolates was conducted. Results CRPA mainly came from the intensive care unit (ICU) and was mostly isolated from sputum samples. The carbapenem resistance rates of P. aeruginosa were 21.37% (2016), 10.62, 5.88, 10 and 13.87% from 2016 to 2020, respectively. Carbapenem-resistant enzymes and aminoglycoside-modifying enzyme-encoding genes were detected in all isolates, and extended-spectrum β-lactamase and cephalosporin enzyme-encoding genes were present in 96.43 and 80.38% of isolates, respectively. The detection rate of OprM showed a statistically significant difference (p < 0.05) between the ICU and other wards. Genes related to biofilms, membrane channel proteins, I integrons and efflux systems were detected in all isolates, with detection rates greater than 90%. CRPA was strongly virulent, and over 80% of isolates carried hypervirulence-associated genes (exoU, exoS, exoT, and exoY). The drug resistance rates of cefepime and piperacillin/tazobactam showed a statistically significant difference (p < 0.05) between strains with exoU (+) and exoU (-) (p < 0.05). Notably, out of the 7 individuals who died, 4 had extensively drug-resistant P. aeruginosa (57.14%). Discussion The detection rates of various resistance and virulence genes were high, and the coexistence phenomenon was serious. In clinical practice, antibiotics should be used reasonably based on different drug resistance genes to ensure the rationality and safety of patient medication.
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Affiliation(s)
- Xin Zhang
- Department of Clinical Laboratory, Children’s Hospital of Soochow University, Suzhou, China
- Institute of Pediatric Research, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China
- Clinical Medical College of Pediatrics, Soochow University, Suzhou, Jiangsu, China
| | - Yunfen Zhu
- Department of Clinical Laboratory, Children’s Hospital of Soochow University, Suzhou, China
| | - Yuanyuan Gao
- Department of Clinical Laboratory, Children’s Hospital of Soochow University, Suzhou, China
| | - Wei Li
- Department of Clinical Laboratory, Children’s Hospital of Soochow University, Suzhou, China
| | - Yunzhong Wang
- Department of Clinical Laboratory, Children’s Hospital of Soochow University, Suzhou, China
- Clinical Medical College of Pediatrics, Soochow University, Suzhou, Jiangsu, China
| | - Yang Li
- Department of Clinical Laboratory, Children’s Hospital of Soochow University, Suzhou, China
- Institute of Pediatric Research, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China
- Clinical Medical College of Pediatrics, Soochow University, Suzhou, Jiangsu, China
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Eltahlawi RA, Jiman-Fatani A, Gad NM, Ahmed SH, Al-Rabia MW, Zakai S, Kharaba A, El-Hossary D. Detection of Carbapenem-resistance in CRE by Comparative Assessment of RAPIDEC ® CARBA NP and Xpert™Carba-R Assay. Infect Drug Resist 2023; 16:1123-1131. [PMID: 36855392 PMCID: PMC9968435 DOI: 10.2147/idr.s393739] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction Carbapenem-resistant Enterobacteriaceae (CRE) infections resist nearly most available antimicrobials, resulting in poor clinical outcomes. Saudi Arabia has a relatively high CRE prevalence. This study aims to evaluate the sensitivity of Rapidec Carba NP test and GeneXpert Carba-R assay compared with conventional manners for detection of carbapenemase-producing Enterobacteriaceae. Methods This is a cross-sectional study including a total of 90 CRE isolates examined at two tertiary hospitals in KSA from October 2020 to December 2021. Gram-negative Enterobacteriaceae were identified by using Vitek 2 system and were furtherly tested for imipenem and meropenem susceptibility by E- test strips, followed by Rapidec Carba NP test and the Xpert™Carba-R assay. Results Carbapenem-resistant K. pneumoniae (78.9%) and carbapenem-resistant E. coli (14.4%) were the two most common isolates species. Colistin (98.9%) and tigecycline (88.9%) were the most effective antibiotics against CRE isolates, followed by amikacin (52.2%), gentamicin (33.3%), cotrimoxazole (15.6%), and ciprofloxacin (8.9%). blaOXA-48 was the predominant carbapenemase gene (44.4%), followed by blaNDM (32.2%). blaKPC gene was not detected. The Rapidec Carba NP and the Xpert™Carba-R demonstrated an overall sensitivity of 69.3% and 88%, respectively, in comparison to gold standard detection of meropenem and imipenem resistance by Vitek 2 system and E- test strips. Discussion RAPIDEC® CARBA NP may be a beneficial screening test for detecting CRE, but for confirmation of the results, Xpert Carba-R assay is more sensitive, significantly lowering the turnaround time compared to reference traditional methods. The information on carbapenemase genes may be used for epidemiologic purposes and outbreak management.
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Affiliation(s)
- Rehab A Eltahlawi
- Department of Microbiology, College of Medicine, Taibah University, Taibah, Saudi Arabia,Department of Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Asif Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Clinical and Molecular Microbiology Laboratory, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Niveen M Gad
- Clinical Microbiology Laboratory, King Fahd Hospital, Medina, Saudi Arabia,Medical Microbiology and Immunology Department, Faculty of Medicine, Benha University, Benha, Egypt
| | - Shereen H Ahmed
- Medical Microbiology and Immunology Department, Faculty of Medicine, Benha University, Benha, Egypt
| | - Mohammed W Al-Rabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Health Promotion Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shadi Zakai
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ayman Kharaba
- Intensive Care Unit, King Fahad Hospital, Madinah, Saudi Arabia
| | - Dalia El-Hossary
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt,Correspondence: Dalia El-Hossary, Email
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Jia J, Huang L, Zhang L, Sheng Y, Chu W, Xu H, Xu A. Genomic characterization of two carbapenem-resistant Serratia marcescens isolates causing bacteremia: Emergence of KPC-2-encoding IncR plasmids. Front Cell Infect Microbiol 2023; 13:1075255. [PMID: 36844412 PMCID: PMC9945258 DOI: 10.3389/fcimb.2023.1075255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/10/2023] [Indexed: 02/11/2023] Open
Abstract
The occurrence and transmission of carbapenemase-producing-Enterobacterales (CPE) on a global scale has become a major issue. Clinical reports are rarely providing information on the genomic and plasmid features of carbapenem-resistant Serratia marcescens. Our objective was to investigate the resistance and transmission dynamics of two carbapenem-resistant S. marcescens that are resistant to carbapenem and have caused bacteremia in China. Blood specimens were taken from two individuals with bacteremia. Multiplex PCR was employed to identify genes that code for carbapenemase. Antimicrobial susceptibility tests and plasmid analysis were conducted on S. marcescens isolates SM768 and SM4145. The genome of SM768 and SM4145 were completely sequenced using NovaSeq 6000-PE150 and PacBio RS II platforms. Antimicrobial resistance genes (ARGs) were predicted using the ResFinder tool. S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and southern blotting were employed to analyze plasmids. Two S. marcescens that produced KPC-2 were identified from bloodstream infections. The antimicrobial susceptibility testing demonstrated that both of the isolates had a resistance to various antibiotics. The whole-genome sequence (WGS) and plasmid analysis revealed the presence of bla KPC-2-bearing IncR plasmids and multiple plasmid-borne antimicrobial resistance genes in the isolates. Our comparative plasmid analysis suggested that the two IncR plasmids identified in this study could be derived from a common ancestor. Our findings revealed the emergence of bla KPC-2-bearing IncR plasmid in China, which could be a hindrance to the transmission of KPC-2-producing S. marcescens in clinical settings.
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Affiliation(s)
- Junli Jia
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lisha Huang
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Long Zhang
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanbing Sheng
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weili Chu
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Aiguo Xu
- Department of Respiratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Aiguo Xu,
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Tavares-Carreon F, De Anda-Mora K, Rojas-Barrera IC, Andrade A. Serratia marcescens antibiotic resistance mechanisms of an opportunistic pathogen: a literature review. PeerJ 2023; 11:e14399. [PMID: 36627920 PMCID: PMC9826615 DOI: 10.7717/peerj.14399] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/25/2022] [Indexed: 01/07/2023] Open
Abstract
Serratia marcescens is a ubiquitous bacterium from order Enterobacterales displaying a high genetic plasticity that allows it to adapt and persist in multiple niches including soil, water, plants, and nosocomial environments. Recently, S. marcescens has gained attention as an emerging pathogen worldwide, provoking infections and outbreaks in debilitated individuals, particularly newborns and patients in intensive care units. S. marcescens isolates recovered from clinical settings are frequently described as multidrug resistant. High levels of antibiotic resistance across Serratia species are a consequence of the combined activity of intrinsic, acquired, and adaptive resistance elements. In this review, we will discuss recent advances in the understanding of mechanisms guiding resistance in this opportunistic pathogen.
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Affiliation(s)
- Faviola Tavares-Carreon
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Karla De Anda-Mora
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Idalia C. Rojas-Barrera
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plön, Germany,Christian-Albrechts-University Kiel, Kiel, Germany
| | - Angel Andrade
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
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Davari N, Khashei R, Pourabbas B, Nikbin VS, Zand F. High frequency of carbapenem-resistant Enterobacteriaceae fecal carriage among ICU hospitalized patients from Southern Iran. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2022; 25:1416-1423. [PMID: 36544530 PMCID: PMC9742572 DOI: 10.22038/ijbms.2022.63099.13938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 10/17/2022] [Indexed: 12/24/2022]
Abstract
Objectives The worldwide emergence of carbapenem-resistant Enterobacteriaceae (CRE) has become a major therapeutic concern to medical institutions. To date, no study has determined the frequency and risk factors of inpatients with CRE fecal carriage in Southern Iran. We studied the features of carbapenemase-producing Enterobacteriaceae (CPE) collected from the central ICU of a university hospital. Materials and Methods Totally, 173 samples, including 124 stool samples from 46 ICU inpatients on admission and different follow-ups, 9 ICU staff, and 40 environmental samples were included. CRE was identified using microbiological methods. Antimicrobial susceptibility was investigated by using the disk diffusion method and E-test. Carbapenemase producers were detected using the mCIM method. Seven carbapenemase genes were characterized. The genetic relationship among 20 CPE was elucidated by PFGE. Results The overall fecal carriage rate was 28.2%, while CRE acquisition was 6.1%. CRE were classified as Klebsiella pneumoniae (71.4%), Escherichia coli (23.8%), and Enterobacter aerogenes (4.8%). From 21 CRE, 20 (95.2%) produced carbapenemases, of which 10, 15, 10, 25, 5, and 65% were blaKPC, blaSME, blaIMP, blaVIM, blaNDM and blaOXA-48-positive, respectively. Out of 20 CPE, 14 different PFGE patterns were observed, categorized into six clusters, suggestive of non-clonal spread. No difference between the examined risk factors with CRE carriage was shown. Conclusion The data indicate a high CRE fecal carriage rate among inpatients. Our findings implicate the widespread of OXA-48 carbapenemase together with heterogeneity among CRE with great concern for dissemination and therapeutic threat. Early diagnosis and monitoring of CRE among inpatients are urgent.
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Affiliation(s)
- Nima Davari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Khashei
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran ,Corresponding authors: Reza Khashei. Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Zand St, Shiraz, Iran. Tel: +98-71-32305410; Fax: +98-71-32304356; ; ; Bahman Pourabbas. Professor Alborzi Clinical Microbiology Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Bahman Pourabbas
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran,Corresponding authors: Reza Khashei. Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Zand St, Shiraz, Iran. Tel: +98-71-32305410; Fax: +98-71-32304356; ; ; Bahman Pourabbas. Professor Alborzi Clinical Microbiology Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran.
| | | | - Farid Zand
- Anesthesiology and Critical Care Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Piccirilli A, Cherubini S, Brisdelli F, Fazii P, Stanziale A, Di Valerio S, Chiavaroli V, Principe L, Perilli M. Molecular Characterization by Whole-Genome Sequencing of Clinical and Environmental Serratia marcescens Strains Isolated during an Outbreak in a Neonatal Intensive Care Unit (NICU). Diagnostics (Basel) 2022; 12:diagnostics12092180. [PMID: 36140580 PMCID: PMC9498040 DOI: 10.3390/diagnostics12092180] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/27/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
The whole-genome sequencing (WGS) of eighteen S. marcescens clinical strains isolated from 18 newborns hospitalized in the Neonatal Intensive Care Unit (NICU) at Pescara Public Hospital, Italy, was compared with that of S. marcescens isolated from cradles surfaces in the same ward. The identical antibiotic resistance genes (ARGs) and virulence factors were found in both clinical and environmental S. marcescens strains. The aac(6′)-Ic, tetA(41), blaSRT-3, adeFGH, rsmA, and PBP3 (D350N) genes were identified in all strains. The SRT-3 enzyme, which exhibited 10 amino acid substitutions with respect to SST-1, the constitutive AmpC β-lactamase in S. marcescens, was partially purified and tested against some β-lactams. It showed a good activity against cefazolin. Both clinical and environmental S. marcescens strains exhibited susceptibility to all antibiotics tested, with the exception of amoxicillin/clavulanate.
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Affiliation(s)
- Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
- Correspondence: (A.P.); (M.P.); Tel.: +39-0862433489 (M.P.)
| | - Sabrina Cherubini
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Fabrizia Brisdelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Paolo Fazii
- Clinical Microbiology and Virology Unit, Pescara Public Hospital, 65122 Pescara, Italy
| | - Andrea Stanziale
- Clinical Microbiology and Virology Unit, Pescara Public Hospital, 65122 Pescara, Italy
| | - Susanna Di Valerio
- Neonatal Intensive Care Unit, Pescara Public Hospital, 65123 Pescara, Italy
| | - Valentina Chiavaroli
- Neonatal Intensive Care Unit, Pescara Public Hospital, 65123 Pescara, Italy
- Liggins Institute, The University of Auckland, Auckland 1141, New Zealand
| | - Luigi Principe
- Clinical Pathology and Microbiology Unit, “S. Giovanni di Dio” Hospital, 88900 Crotone, Italy
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
- Correspondence: (A.P.); (M.P.); Tel.: +39-0862433489 (M.P.)
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Zou H, Berglund B, Wang S, Zhou Z, Gu C, Zhao L, Meng C, Li X. Emergence of bla NDM-1, bla NDM-5, bla KPC-2 and bla IMP-4 carrying plasmids in Raoultella spp. in the environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119437. [PMID: 35537555 DOI: 10.1016/j.envpol.2022.119437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
To date, carbapenem-resistant Enterobacteriaceae have been found predominantly in clinical settings worldwide. Raoultella belongs to the Enterobacteriaceae family which can cause hospital-acquired infections, and carbapenem-resistant Raoultella spp. (CRR) is sporadically reported in the environment. We investigated the distribution and underlying resistance mechanisms of CRR in a wastewater treatment plant (WWTP) from eastern China between January 2018 and February 2019. A total of 17 CRR were isolated from 324 environmental samples, including Raoultella ornithinolytica (n = 15) and Raoultella planticola (n = 2). The detection of CRR was more frequent in the water inlet compared to anaerobic tank, aerobic tank, sludge thickener, activated sludge, mud cake storage area, and water outlet, and CRR was detected in mud cake stacking area. All CRR were resistant to imipenem, meropenem, ampicillin, piperacillin-tazobactam, cefotaxime, ceftazidime, trimethoprim-sulfamethoxazole and fosfomycin. Four different carbapenemase genes were identified, including blaKPC-2 (n = 13), blaNDM-1 (n = 8), blaNDM-5 (n = 1), blaIMP-4 (n = 1). Interestingly, isolated R. ornithinolytica from the WWTP were closely related to those reported from human samples in China. Plasmid analysis indicated that IncFII(Yp), IncP6, and IncU mediated blaKPC-2 spread, IncX3 and IncN2 mediated blaNDM spread in the environment. The core structure of the Tn3-ISKpn27-blaKPC-2-ISKpn6, ISAba125-blaNDM-bleMBL-trpF-dsbD were identified. The study provides evidence that Raoultella spp. may spread alarming carbapenem resistance in the environment and, therefore, the continuous surveillance for carbapenem resistance in the WWTP should be conducted, especially sludge.
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Affiliation(s)
- Huiyun Zou
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Björn Berglund
- Department of Clinical and Experimental Medicine, Linköping University, 581 85, Linköping, Sweden
| | - Shuang Wang
- Institute of Infection Disease Control, Shandong Centre for Disease Control and Prevention, Jinan, China
| | - Ziyu Zhou
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Congcong Gu
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ling Zhao
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Chen Meng
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
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Rectal and Tracheal Carriage of Carbapenemase Genes and Class 1 and 2 Integrons in Patients in Neurosurgery Intensive Care Unit. Antibiotics (Basel) 2022; 11:antibiotics11070886. [PMID: 35884140 PMCID: PMC9312170 DOI: 10.3390/antibiotics11070886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
The spread of multidrug-resistant Gram-negative bacteria, which is associated with the distribution of beta-lactamase genes and class 1 and 2 integrons, is a global problem. In this study, in the Moscow neurosurgery intensive care unit (neuro-ICU), the high prevalence of the above-stated genes was found to be associated with intestinal and tracheal carriage. Seven-point prevalence surveys, which included 60 patients in the neuro-ICU, were conducted weekly in the period from Oct. to Nov. 2019. A total of 293 clinical samples were analyzed, including 146 rectal and 147 tracheal swabs; 344 Gram-negative bacteria isolates were collected. Beta-lactamase genes (n = 837) were detected in the isolates, including beta-lactamase blaTEM (n = 162), blaSHV (n = 145), cephalosporinase blaCTX–M (n = 228), carbapenemase blaNDM (n = 44), blaKPC (n = 25), blaOXA–48 (n = 126), blaOXA–51–like (n = 54), blaOXA–40-like (n = 43), blaOXA–23-like (n = 8), and blaVIM (n = 2), as well as class 1 (n = 189) and class 2 (n = 12) integrons. One extensively drug-resistant Klebsiella pneumoniae strain (sequence type ST39 and capsular type K23), simultaneously carried beta-lactamase genes, blaSHV–40 and blaTEM–1B, three carbapenemase genes, blaNDM, blaKPC, and blaOXA–48, the cephalosporinase gene blaCTX–M, and two class 1 integrons. Before this study, such heavily armed strains have not been reported, suggesting the ongoing evolution of antibiotic resistance.
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11
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Chen L, Ai W, Zhou Y, Wu C, Guo Y, Wu X, Wang B, Rao L, Xu Y, Zhang J, Chen L, Yu F. Outbreak of IncX8 Plasmid-Mediated KPC-3-Producing Enterobacterales Infection, China. Emerg Infect Dis 2022; 28:1421-1430. [PMID: 35731165 PMCID: PMC9239885 DOI: 10.3201/eid2807.212181] [Citation(s) in RCA: 1] [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] [Indexed: 11/19/2022] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) infection is highly endemic in China; Klebsiella pneumoniae carbapenemase (KPC) 2-producing CRE is the most common, whereas KPC-3-producing CRE is rare. We report an outbreak of KPC-3-producing Enterobacterales infection in China. During August 2020-June 2021, 25 blaKPC-3-positive Enterobacteriale isolates were detected from 24 patients in China. Whole-genome sequencing analysis revealed that the blaKPC-3 genes were harbored by IncX8 plasmids. The outbreak involved clonal expansion of KPC-3-producing Serratia marcescens and transmission of blaKPC-3 plasmids across different species. The blaKPC-3 plasmids demonstrated high conjugation frequencies (10-3 to 10-4). A Galleria mellonella infection model showed that 2 sequence type 65 K2 K. pneumoniae strains containing blaKPC-3 plasmids were highly virulent. A ceftazidime/avibactam in vitro selection assay indicated that the KPC-3-producing strains can readily develop resistance. The spread of blaKPC-3-harboring IncX8 plasmids and these KPC-3 strains should be closely monitored in China and globally.
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12
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Chiș AA, Rus LL, Morgovan C, Arseniu AM, Frum A, Vonica-Țincu AL, Gligor FG, Mureșan ML, Dobrea CM. Microbial Resistance to Antibiotics and Effective Antibiotherapy. Biomedicines 2022; 10:biomedicines10051121. [PMID: 35625857 PMCID: PMC9138529 DOI: 10.3390/biomedicines10051121] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/24/2022] Open
Abstract
Currently, the efficacy of antibiotics is severely affected by the emergence of the antimicrobial resistance phenomenon, leading to increased morbidity and mortality worldwide. Multidrug-resistant pathogens are found not only in hospital settings, but also in the community, and are considered one of the biggest public health concerns. The main mechanisms by which bacteria develop resistance to antibiotics include changes in the drug target, prevention of entering the cell, elimination through efflux pumps or inactivation of drugs. A better understanding and prediction of resistance patterns of a pathogen will lead to a better selection of active antibiotics for the treatment of multidrug-resistant infections.
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13
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Das S, Vishakha K, Banerjee S, Nag D, Ganguli A. Exploring the antibacterial, antibiofilm, and antivirulence activities of tea tree oil-containing nanoemulsion against carbapenem-resistant Serratia marcescens associated infections. BIOFOULING 2022; 38:100-117. [PMID: 35012385 DOI: 10.1080/08927014.2021.2022125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Carbapenem-resistant Serratia marcescens (CRE-S. marcescens) has recently emerged as an opportunistic human pathogen that causes various nosocomial and respiratory tract infections. The prognosis for CRE-S. marcescens-related infections is very poor and these infections are difficult to treat. This study investigated the synthesis of tea tree oil nanoemulsion (TTO-NE) and its impact on CRE-S. marcescens both in vitro and in vivo. TTO-NE was characterized by dynamic light scattering (DLS) and effectively eradicated bacterial planktonic and sessile forms, reduced bacterial virulence factors, and generated reactive oxygen species (ROS) in the bacterial cell. Notably, TTO-NE was efficient in reducing the colonization of CRE-S. marcescens in a C. elegans in vivo model. The data suggest that TTO-NE might be an excellent tool to combat infections associated with CRE-S. marcescens.
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Affiliation(s)
- Shatabdi Das
- Department of Microbiology, Techno India University, Kolkata, West Bengal, India
| | - Kumari Vishakha
- Department of Microbiology, Techno India University, Kolkata, West Bengal, India
| | - Satarupa Banerjee
- Department of Microbiology, Techno India University, Kolkata, West Bengal, India
| | - Debasish Nag
- Department of Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| | - Arnab Ganguli
- Department of Microbiology, Techno India University, Kolkata, West Bengal, India
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14
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Li D, Zhang X, Wang Y, Xue J, Ji X, Shao X, Li Y. Epidemiology and Drug Resistance of Pathogens Isolated from Cerebrospinal Fluids at a Children's Medical Center in Eastern China During 2006-2020. Infect Drug Resist 2021; 14:5417-5428. [PMID: 34949927 PMCID: PMC8689011 DOI: 10.2147/idr.s344720] [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: 10/16/2021] [Accepted: 12/03/2021] [Indexed: 11/23/2022] Open
Abstract
Objective To investigate the epidemiology and drug resistance of pathogens isolated from cerebrospinal fluid samples at a children's medical center in eastern China and provide the basis for anti-infection treatments. Methods In all, 307 non-duplicated strains of pathogens were isolated from cerebrospinal fluid samples in the Children's Hospital of Soochow University from January 2006 to December 2020. Mass spectrometry was used for pathogen identification. The VITEK 2 Compact system and Kirby-Bauer method were applied to determine antimicrobial susceptibility. Results Among the 307 isolates, gram-positive bacteria, gram-negative bacteria and fungi accounted for 60.26%, 34.53%, and 5.21%, respectively. The most prevalent pathogens were Streptococcus pneumoniae (26.06%), Escherichia coli (20.20%) and Streptococcus agalactiae (17.26%). The number of isolates was highest in winter. The most prevalent gram-positive bacterium in children <6 months old was Streptococcus agalactiae, while Streptococcus pneumoniae was the most in children were >6 months old. The drug resistance of gram-positive bacteria, fungi and Haemophilus influenza were not high. In addition, 35 strains of gram-negative bacteria produced extended-spectrum β-lactamases (ESBLs) and 6 strains were identified as multidrug-resistant (MDR) bacteria. These strains showed much higher resistance to the antibiotics than other strains. Conclusion Cases of meningitis among children have increased in the past 15 years and MDR bacteria were also identified. The emergence of MDR bacteria is a cause for great concern and requires further investigation.
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Affiliation(s)
- Dan Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Xin Zhang
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China.,Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China
| | - Yunzhong Wang
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China
| | - Jian Xue
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China
| | - Xueqiang Ji
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China
| | - Xuejun Shao
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China.,Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China.,Clinical Medical College of Pediatrics, Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China
| | - Yang Li
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China.,Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China.,Clinical Medical College of Pediatrics, Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China
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15
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Li X, He J, Jiang Y, Peng M, Yu Y, Fu Y. Genetic Characterization and Passage Instability of a Hybrid Plasmid Co-Harboring blaIMP-4 and blaNDM-1 Reveal the Contribution of Insertion Sequences During Plasmid Formation and Evolution. Microbiol Spectr 2021; 9:e0157721. [PMID: 34908434 PMCID: PMC8672901 DOI: 10.1128/spectrum.01577-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/04/2021] [Indexed: 01/20/2023] Open
Abstract
Carbapenemase is the predominant enzyme in the mechanism leading to Enterobacterales resistance to carbapenems, but only a limited number of isolates harbor double classes/types of carbapenemase. Here, an IMP-4 and NDM-1 producer named Klebsiella michiganensis 7525 is reported, and the co-harboring plasmid is further characterized. K. michiganensis 7525 was positive for the blaIMP-4 and blaNDM-1 genes by the NG-Test Carba-5 method and PCR followed by sequencing, and both were located on the same plasmid (designated pKOX7525_1) according to S1-PFGE with Southern blot experiments. pKOX7525_1 was capable of transconjugation with an efficiency of 4.3 × 10-8 in a filter mating experiment. Whole-genome sequencing and bioinformatics analysis confirmed that the plasmid was novel, clustered to the incompatibility type of IncHIB/IncFIA/IncR and presented high similarity to a blaIMP-4-carrying IncHIB plasmid (pA) published with 79% coverage and 100% sequence identify. In contrast, a large-fragment insertion and inversion mediated by IS26 was observed on the plasmid, which introduced a genetic hybrid zone with multiple resistance genes, including blaNDM-1, to the plasmid. In the transconjugants, the presence of pKOX7525_1 had a negative impact on bacterial fitness. In vitro evolution experiments showed that pKOX7525_1 in the transconjugant could not be stably inherited after 10 days of passage and that blaNDM-1 could be lost during repeated laboratory passage. Our study not only reports a novel plasmid co-harboring blaIMP-4 and blaNDM-1 but also highlights the putative pathway of plasmid formation and evolution by means of genetic rearrangement through sequence insertion and homologue recombination, which may have critical value for plasmid research and increase awareness of carbapenem-resistant Enterobacteriaceae (CRE). IMPORTANCE In this study, we characterized a novel plasmid from a carbapenem-resistant K. michiganensis (CRKM) isolate, which harbors two metallo-β-lactamases (MBLs), IMP-4 and NDM-1, is capable of transconjugation and contains three replicons. Our results first expand the diversity of plasmids co-harboring carbapenemase genes in Enterobacterales, which exhibits epidemic importance in bacterial resistance. Additionally, we investigated the origin and formation of this MBL double-positive plasmid based on comparative genomics analysis, which indicated that IS26 plays a vital role through continuous genetic rearrangements. Moreover, this plasmid is unstable in transconjugants during passage at the multidrug-resistant (MDR) region of blaNDM-1, with fluctuating stability under varying antibiotic selection, highlighting auspicious considerations regarding recognition of the complexity and plasticity of plasmids in evolution and re-emphasizing clinical infection control inspired by CRE.
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Affiliation(s)
- Xi Li
- Centre of Laboratory Medicine, Zhejiang Provincial People’s Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Minfei Peng
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Linhai, Zhejiang Province, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Fu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
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16
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Hagras SAA, Hosny AEDMS, Helmy OM, Salem-Bekhit MM, Shakeel F, Farrag HA. Effect of sub-inhibitory concentrations of cefepime on biofilm formation by Pseudomonas aeruginosa. Can J Microbiol 2021; 67:894-901. [PMID: 34731576 DOI: 10.1139/cjm-2021-0229] [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: 11/22/2022]
Abstract
This study investigated the effect of cefepime at sub-minimum inhibitory concentrations (sub-MICs) on in vitro biofilm formation (BF) by clinical isolates of Pseudomonas aeruginosa. The effect of cefepime at sub-MIC levels (½-1/256 MIC) on in vitro BF by six clinical isolates of P. aeruginosa was phenotypically assessed following 24 and 48 h of challenge using the tissue culture plate (TCP) assay. Quantitative real-time polymerase chain reaction (qRT-PCR) was employed to observe the change in expression of three biofilm-related genes, namely, a protease-encoding gene (lasA), fimbrial protein-encoding gene (cupA1), and alginate-encoding gene (algC), in a weak biofilm-producing strain of P. aeruginosa following 24 and 48 h of challenge with sub-MICs of cefepime. The BF morphology in response to cefepime was imaged using scanning electron microscopy (SEM). The TCP assay showed strain-, time-, and concentration-dependent changes in in vitro BF in P. aeruginosa following challenge with sub-MICs of cefepime, with a profound increase in strains with inherently no or weak biofilm-producing ability. RT-PCR revealed time-dependent upregulation in the expression of the investigated genes following challenge with ½ and ¼ MIC levels, as confirmed by SEM. Cefepime at sub-MICs could upregulate the expression of BF-related genes and enhance BF by P. aeruginosa clinical isolates.
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Affiliation(s)
- Soheir A A Hagras
- Department of Drug Radiation Research, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority, Cairo, Egypt.,Inaya Medical Colleges, Riyadh, Saudi Arabia
| | - Alaa El-Dien M S Hosny
- Department of Microbiology & Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Omneya M Helmy
- Department of Microbiology & Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mounir M Salem-Bekhit
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.,Department of Microbiology & Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Faiyaz Shakeel
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hala A Farrag
- Department of Drug Radiation Research, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority, Cairo, Egypt
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17
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de Medeiros Azevedo T, Aburjaile FF, Ferreira-Neto JRC, Pandolfi V, Benko-Iseppon AM. The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications. World J Microbiol Biotechnol 2021; 37:206. [PMID: 34708327 DOI: 10.1007/s11274-021-03168-2] [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: 07/22/2021] [Accepted: 10/05/2021] [Indexed: 11/25/2022]
Abstract
Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.
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Affiliation(s)
- Thamara de Medeiros Azevedo
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Flávia Figueira Aburjaile
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - José Ribamar Costa Ferreira-Neto
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Valesca Pandolfi
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil.
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18
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Huang F, Li S, Lou L, Mo J, Xu H. Comparative Genomic Analysis and Phenotypic Characterization of Bronchoscope-Associated Klebsiella aerogenes. Pol J Microbiol 2021; 70:409-412. [PMID: 34584536 PMCID: PMC8459003 DOI: 10.33073/pjm-2021-038] [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: 06/06/2021] [Revised: 07/21/2021] [Accepted: 08/04/2021] [Indexed: 11/05/2022] Open
Abstract
Bronchoscopes have been linked to outbreaks of nosocomial infections. The phenotypic and genomic profiles of bronchoscope-associated Klebsiella aerogenes isolates are largely unknown. In this work, a total of 358 isolates and 13 isolates were recovered from samples after clinical procedures and samples after decontamination procedures, respectively, over the five months. Antimicrobial susceptibility testing found seven K. aerogenes isolates exhibiting a low-level resistance to antimicrobial agents. Among seven K. aerogenes isolates, we found five sequence types (STs) clustered into three main clades. Collectively, this study described for the first time the phenotypic and genomic characteristics of bronchoscope-associated K. aerogenes.
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Affiliation(s)
- Fang Huang
- Disinfection and Sterilization Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shuang Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lan Lou
- Disinfection and Sterilization Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Junjun Mo
- Disinfection and Sterilization Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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19
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Sun M, Xiao W, Xu Q. IncN1 ST7 Epidemic Plasmid Carrying blaIMP-4 in One ST85-Type Klebsiella oxytoca Clinical Isolate with Porin Deficiency. Infect Drug Resist 2021; 14:3827-3835. [PMID: 34566416 PMCID: PMC8458025 DOI: 10.2147/idr.s330362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/07/2021] [Indexed: 01/07/2023] Open
Abstract
Purpose Klebsiella oxytoca is an opportunistic pathogen causing nosocomial infections. This study was designed to characterize the genomic features of a carbapenem-resistant K. oxytoca strain and analyze its molecular characteristics. Materials and Methods The strain wzx-IMP was isolated from the blood of a 2-year-old girl diagnosed with acute myeloid leukemia-M7. Species identification was performed, and the minimal inhibitory concentration of the strain was measured. Multilocus sequence typing was performed to identify the subtypes of K. oxytoca. The transfer capacity of the blaIMP-4-harboring plasmid was investigated by conjugation experiments, and the genome characteristics of the strain were examined using whole-genome sequencing. Results wzx-IMP belongs to the ST85 type and is resistant to imipenem and meropenem, which harbored the blaIMP-4 gene. The blaIMP-4 gene was located in an IS26-associated class 1 integron of pwzx_IMP, which contains conserved IncN1-type backbone regions with a replication gene and its accessory structure for plasmid replication. The blaIMP-4-carrying plasmid in wzx-IMP was successfully transferred to Escherichia coli EC600 by conjugation. Whole-genome sequencing showed that the wzx-IMP isolate included the blaOXY-1-1 gene, accompanied by OmpK36 absence. Conclusion We report an ST85-type carbapenem-resistant K. oxytoca strain, which produces blaIMP-4 located in an IncN1-type plasmid and accompanied by OmpK36 porin deficiency.
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Affiliation(s)
- Mingyue Sun
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, People's Republic of China
| | - Weiqiang Xiao
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, People's Republic of China
| | - Qingxia Xu
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, People's Republic of China
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20
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Li Y, Li D, Xue J, Ji X, Shao X, Yan J. The Epidemiology, Virulence and Antimicrobial Resistance of Invasive Klebsiella pneumoniae at a Children's Medical Center in Eastern China. Infect Drug Resist 2021; 14:3737-3752. [PMID: 34548798 PMCID: PMC8449645 DOI: 10.2147/idr.s323353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/02/2021] [Indexed: 12/28/2022] Open
Abstract
Objective This study investigated the epidemiology, virulence and drug resistance of invasive Klebsiella pneumoniae (K. pneumoniae) isolates at a children’s medical center in eastern China in order to obtain epidemiologic, virulence, and antimicrobial resistance data that can guide for the selection and development of anti-infection treatments. Methods A total of 94 invasive K. pneumoniae strains were isolated from children between January 2016 and December 2020 at the Children’s Hospital of Soochow University. The strains were identified by mass spectrometry. The Kirby–Bauer method and VITEK 2 Compact system were used to analyze the antimicrobial susceptibility. Polymerase chain reaction (PCR) and sequencing was performed to detect the capsular serotypes, virulence-associated genes, β-lactam antibiotic resistance genes and multilocus sequence typing. Results The PCR results showed that 87 strains (92.55%) of invasive K. pneumoniae were hypervirulent capsular serotypes, with K57 as the dominant capsular serotype (62.77%). All strains carried virulence-associated genes. Among them, 84 strains (89.36%) carried hypervirulence genes, with iroB (86.17%) being the predominant; meanwhile, other virulence genes, including wabG (100.00%), mrkD (98.94%), ycfM (96.81%), fimH (95.74%) and Uge (88.30%), were detected in most strains. All strains carried β-lactam antibiotic resistance genes; the main extended-spectrum β-lactamase gene was blaSHV-11 (86.17%) and the major AmpC cephalosporinase genes were blaFOX-1 (86.17%) and blaACT-1 (70.21%). Carbapenemase genes were detected in only a few isolates. Notably, 12 invasive K. pneumoniae isolates were identified as carbapenem-resistant and hypervirulent K. pneumoniae (CR-HVKP), and 14 other multidrug resistance (MDR) isolates were also detected. Conclusion The results of this study reveal the epidemiology, virulence and antimicrobial resistance of invasive K. pneumoniae in pediatric patients. Both CR-HVKP and MDR strains were identified, which should be of great concern to clinicians.
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Affiliation(s)
- Yang Li
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, People's Republic of China.,Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, People's Republic of China.,Division of Basic Medical Microbiology, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, People's Republic of China.,Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China
| | - Dan Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Jian Xue
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China
| | - Xueqiang Ji
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China
| | - Xuejun Shao
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, People's Republic of China
| | - Jie Yan
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, People's Republic of China.,Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, People's Republic of China.,Division of Basic Medical Microbiology, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, People's Republic of China
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21
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Yang Y, Liu J, Muhammad M, Liu H, Min Z, Lu J, Zhang L, Chai Z. Factors behind the prevalence of carbapenem-resistant Klebsiella pneumoniae in pediatric wards. Medicine (Baltimore) 2021; 100:e27186. [PMID: 34516520 PMCID: PMC8428699 DOI: 10.1097/md.0000000000027186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 07/09/2021] [Accepted: 08/22/2021] [Indexed: 01/05/2023] Open
Abstract
ABSTRACT The emergence of carbapenem-resistant Enterobacteriaceae made the treatment difficult, which has become a significant issue of public health. A sharp increase of carbapenem-resistance rate in Klebsiella pneumoniae was observed in a maternity and child health care hospital in Zunyi, China, in 2014.In 2015 to 2016, carbapenem-resistant Klebsiella pneumoniae (CRKp) isolated from all the clinical samples were analyzed to identify the carbapenem-resistance genes. They were then fingerprinted in order to determine their genetic relationship. Clinical data such as usage of imipenem in 2012 to 2016 and the nosocomial infection surveillance data were analyzed.Thirty-five isolates of CRKp out of 4328 various pathogens were obtained, and blaNDM-1 was identified to be the most common resistant gene present in the CRKp isolates. The fingerprint analysis identified 15 major clusters of CRKp isolates. The bacteria with close proximity relationship tended to be from the same wards. However, a few CRKp isolates from different wards were found to be genetically highly related. The clinical data showed a significantly higher usage of carbapenems in 2012 to 2013 before the CRKp rate sharply increased in 2014. The nosocomial infection surveillance showed an unexpectedly high rate of failures to meet the requirement of the hospital environment hygiene and hand hygiene in the neonatal ward.The increasing isolation rate of CRKp was associated with poorly regulated usage of carbapenems, impropriate medical practices, and the poor hospital environmental hygiene and hand hygiene.
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Affiliation(s)
- Yuxin Yang
- Department of Pathology, Zunyi Maternity and Child Health Care Hospital, Zunyi, Guizhou, China
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Jia Liu
- Department of Pharmacy, Zunyi Maternity and Child Health Care Hospital, Zunyi, Guizhou, China
| | - Murad Muhammad
- Department of Surgery (RMH), University of Melbourne, Melbourne, Victoria, Australia
| | - Hanting Liu
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, Shanxi, China
| | - Zongsu Min
- Department of Pathology, Zunyi Maternity and Child Health Care Hospital, Zunyi, Guizhou, China
| | - Jing Lu
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Lei Zhang
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, Shanxi, China
- Artificial Intelligence and Modelling in Epidemiology Program, Melbourne Sexual Health Centre, Alfred Health, Melbourne, Australia
- Central Clinical School, Faculty of Medicine, Monash University, Melbourne, Australia
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhonglin Chai
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
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22
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Cortés-Ortíz IA, Mendieta-Condado E, Escobar-Escamilla N, Juárez-Gómez JC, Garcés-Ayala F, Rodriguez AA, Bravata-Alcántara JC, Gutiérrez-Muñoz VH, Bello-López JM, Ramírez–González JE. Multidrug-resistant Raoultella ornithinolytica misidentified as Klebsiella oxytoca carrying blaOXA β-lactamases: antimicrobial profile and genomic characterization. Arch Microbiol 2021; 203:5755-5761. [DOI: 10.1007/s00203-021-02515-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 11/28/2022]
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23
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Bes T, Nagano D, Martins R, Marchi AP, Perdigão-Neto L, Higashino H, Prado G, Guimaraes T, Levin AS, Costa S. Bloodstream Infections caused by Klebsiella pneumoniae and Serratia marcescens isolates co-harboring NDM-1 and KPC-2. Ann Clin Microbiol Antimicrob 2021; 20:57. [PMID: 34461917 PMCID: PMC8404334 DOI: 10.1186/s12941-021-00464-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 08/16/2021] [Indexed: 11/10/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae are a worldwide health problem and isolates carrying both blaKPC-2 and blaNDM-1 are unusual. Here we describe the microbiological and clinical characteristics of five cases of bloodstream infections (BSI) caused by carbapenem-resistant Klebsiella pneumoniae and Serratia marcescens having both blaKPC-2 and blaNDM-1. Of the five blood samples, three are from hematopoietic stem cell transplantation patients, one from a renal transplant patient, and one from a surgical patient. All patients lived in low-income neighbourhoods and had no travel history. Despite antibiotic treatment, four out of five patients died. The phenotypic susceptibility assays showed that meropenem with the addition of either EDTA, phenylboronic acid (PBA), or both, increased the zone of inhibition in comparison to meropenem alone. Molecular tests showed the presence of blaKPC-2 and blaNDM-1 genes. K. pneumoniae isolates were assigned to ST258 or ST340 by whole genome sequencing. This case-series showed a high mortality among patients with BSI caused by Enterobacteriae harbouring both carbapenemases. The detection of carbapenemase-producing isolates carrying both blaKPC-2 and blaNDM-1 remains a challenge when using only phenotypic assays. Microbiology laboratories must be alert for K. pneumoniae isolates producing both KPC-2 and NDM-1.
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Affiliation(s)
- Taniela Bes
- Infectious Diseases Division, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil. .,Institute of Tropical Medicine of the University of São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470; LIM 49, São Paulo, CEP 05403-000, Brazil.
| | - Debora Nagano
- Institute of Tropical Medicine of the University of São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470; LIM 49, São Paulo, CEP 05403-000, Brazil
| | - Roberta Martins
- Institute of Tropical Medicine of the University of São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470; LIM 49, São Paulo, CEP 05403-000, Brazil
| | - Ana Paula Marchi
- Institute of Tropical Medicine of the University of São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470; LIM 49, São Paulo, CEP 05403-000, Brazil
| | - Lauro Perdigão-Neto
- Infectious Diseases Division, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil.,Institute of Tropical Medicine of the University of São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470; LIM 49, São Paulo, CEP 05403-000, Brazil.,Infection Control, Hospital das Clínicas Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Hermes Higashino
- Infectious Diseases Division, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil
| | - Gladys Prado
- Institute of Tropical Medicine of the University of São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470; LIM 49, São Paulo, CEP 05403-000, Brazil
| | - Thais Guimaraes
- Infectious Diseases Division, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil.,Infection Control, Hospital das Clínicas Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Anna S Levin
- Infectious Diseases Division, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil.,Institute of Tropical Medicine of the University of São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470; LIM 49, São Paulo, CEP 05403-000, Brazil.,Infection Control, Hospital das Clínicas Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Silvia Costa
- Infectious Diseases Division, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil.,Institute of Tropical Medicine of the University of São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470; LIM 49, São Paulo, CEP 05403-000, Brazil.,Infection Control, Hospital das Clínicas Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
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24
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Wang X, Xiao W, Li L, Jing M, Sun M, Chang Y, Qu Y, Jiang Y, Xu Q. Analysis of the molecular characteristics of a blaKPC-2-harbouring untypeable plasmid in Serratia marcescens. Int Microbiol 2021; 25:237-244. [PMID: 34232406 DOI: 10.1007/s10123-021-00172-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Serratia marcescens has attracted increasing attention worldwide as a neglected opportunistic pathogen of public health concern, especially due to its antimicrobial resistance features, which usually cause nosocomial infections in immunocompromised or critically ill patients. METHODS In our study, four carbapenem-resistant Serratia marcescens (CRSM) clinical isolates were characterized in our hospital from February 2018 to May 2018. The conjugation experiment confirmed the transferability of the carbapenem resistance gene. The types of carbapenem resistance genes were detected by PCR. The homology of the strains was analysed by pulsed field gel electrophoresis (PFGE). The characteristics of the plasmid and environment of carbapenem resistance genes were analysed after whole genome sequencing was performed. Then, we compared the amino acid sequence of the replication initiation protein and constructed a dendrogram by the neighbour-joining method. RESULTS All four isolates showed carbapenem resistance conferred by a blaKPC-2-harbouring plasmid. They had exactly the same bands confirmed by PFGE and were defined as the homologous strains. The blaKPC-2 genes in all of the isolates were located in a 42,742 bp plasmid, which was located in the core region of antibiotic resistance and was composed of Tn3 family transposons, recombinant enzyme genes, ISKpn6 and ISKpn27. The core region of antibiotic resistance formed a 'Tn3-ISKpn6-blaKPC-ISKpn27-Tn3' structure, which was an independent region as a movable element belonging to transposon Tn6296 and its derivatives. The plasmid had a similar skeleton to incX6 plasmids and a similar amino acid sequence to the replication initiation protein. The plasmid was defined as an untypeable blaKPC-2-harbouring plasmid named the 'IncX6-like' plasmid. CONCLUSION The four CRSM isolates were mainly clonally disseminated with a blaKPC-2-harbouring plasmid in our hospital. The pKPC-2-HENAN1602 plasmid (CP047392) in our study was first reported in Serratia marcescens, which belongs to an untypeable group named the 'IncX6-like' plasmid. The carbapenem-resistant gene structure surrounding blaKPC-2 as a sole accessory module can be acquired by horizontal gene transfer and might lead to serious nosocomial infection.
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Affiliation(s)
- Xiaokun Wang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Weiqiang Xiao
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Lu Li
- Department of Anesthesiology and Perioperative Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Min Jing
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Mingyue Sun
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Yanmin Chang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Yuanye Qu
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Yu Jiang
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China
| | - Qingxia Xu
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China. .,Department of Zhengzhou Key Laboratory of Digestive Tumor Markers, No.127 Dongming Road Jinshui District, Zhengzhou, 450008, Henan, People's Republic of China.
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25
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Zhu Y, Jia P, Li X, Wang T, Zhang J, Zhang G, Duan S, Kang W, Xu Y, Yang Q. Carbapenemase detection by NG-Test CARBA 5-a rapid immunochromatographic assay in carbapenem-resistant Enterobacterales diagnosis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:769. [PMID: 34268382 PMCID: PMC8246204 DOI: 10.21037/atm-20-8216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/05/2021] [Indexed: 11/08/2022]
Abstract
Background The global spread of carbapenem-resistant Enterobacterales (CRE) represents a serious public health concern as these organisms are associated with limited treatment options, high mortality rate and rapid transmissibility. The identification of carbapenemase remains a challenge in microbiological laboratories as no single method is perfect when considering cost, carbapenemase coverage, accuracy, handling complexity and TATs together. Methods NG-Test CARBA 5 assay and modified carbapenem inactivation method in conjunction with EDTA carbapenem inactivation method (mCIM/eCIM) were challenged with a collection of 299 molecularly characterized CRE isolates in China in order to evaluate the performance in detecting five major carbapenemases (blaKPC, blaNDM, blaVIM, blaIMP, and blaOXA-48) among Enterobacterales. Results NG-Test CARBA 5 detected all KPC-, NDM-, VIM- and OXA-48-producing isolates perfectly with a weak false-positive signal for NDM in an IMP-4 producer, which makes the specificity for NDM decreases to 99.6%. The overall specificity/sensitivity were 99.9%/100% for NG-Test CARBA 5. mCIM/eCIM achieved high specificity of 100%/100% and sensitivity of 99.6%/97.4%, with one S. marcescens isolate harboring VIM-2 undetected. Conclusions Both NG-Test CARBA 5 and mCIM/eCIM showed excellent results in the tested carbapenemase (blaKPC, blaNDM, blaVIM, blaIMP, and blaOXA-48) detection compared with molecular genotypic test. As every assay has its own limitations, suitable methods should be combined for the establishment of the CRE diagnostic pathways.
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Affiliation(s)
- Ying Zhu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Graduate school, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Peiyao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Graduate school, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xue Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Clinical Laboratory, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Tong Wang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingjia Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ge Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Simeng Duan
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Kang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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26
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Zhang J, Jia P, Zhu Y, Zhang G, Xu Y, Yang Q. Performance Evaluation of BD Phoenix NMIC-413 Antimicrobial Susceptibility Testing Panel for Imipenem, Meropenem, and Ertapenem Against Clinical Carbapenem-Resistant and Carbapenem-Susceptible Enterobacterales. Front Med (Lausanne) 2021; 8:643194. [PMID: 33937287 PMCID: PMC8079628 DOI: 10.3389/fmed.2021.643194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/22/2021] [Indexed: 12/30/2022] Open
Abstract
Purpose: The infection of carbapenem-resistant Enterobacterales (CRE) has become a major clinical and healthcare problem worldwide. The screening methods of CRE have been extensively developed but still need improving [e.g., tests with accurate and simple minimum inhibitory (MICs)]. In this study, the performance of the BD Phoenix NMIC-413 AST panel was evaluated against clinical CRE and carbapenem-susceptible Enterobacterales (CSE) in China. The panel was first evaluated in the Chinese clinical lab. Methods: Antimicrobial susceptibility testing of 303 clinical Enterobacterales isolates were conducted by broth microdilution (BMD), Phoenix NMIC-413 AST panel, and disk diffusion method for imipenem, ertapenem, and meropenem. Considering BMD is a gold standard, essential agreement (EA), categorical agreement (CA), minor error (MIE), major error (ME), and very major error (VME) were determined according to CLSI guidelines. CA and EA > 90%, ME <3%, and VME <1.5% were considered as acceptable criteria. Polymerase chain reaction and sanger sequencing were performed to determine the β-lactamase genotypes of CRE isolates. Results: Three hundred and three isolates included 195 CREs and 108 CSEs were enrolled according to the BMD-MIC values of three carbapenems. Tested CREs showing 100 blaKPC−2-positive organisms, 31 blaIMP-positive organisms, 28 blaNDM-positive organisms, 5 blaVIM-positive organisms, 2 both blaIMP and blaVIM-positive organisms, 2 blaOXA−48-positive organisms, and 27 isolates without carbapenemase genes. For the Phoenix NMIC-413 method, CA and EA rates >93%, MIE rates <5%, ME rates <1.75%, and VME rates were 0%, across the three drugs. For the disk diffusion method, the CA rates for three drugs were all >93%, while the MIE and ME rates were all <5 and <3%, respectively. VME rate was 3.28% for imipenem, exceeded the cut-off value specified by CLSI M52, 0 and 0.56% for ertapenem and meropenem, separately. Conclusion: Based on the genomic data, the detection of CRE and CSE was more reliable using the BD Phoenix NMIC-413 panel compared to the BMD and disk approaches. Therefore, our study supports the use of BD Phoenix NMIC-413 panel as a suitable alternative to BMD for the detection of carbapenem resistant isolates in a clinical setting.
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Affiliation(s)
- Jingjia Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Peiyao Jia
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Zhu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ge Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Vrancianu CO, Dobre EG, Gheorghe I, Barbu I, Cristian RE, Chifiriuc MC. Present and Future Perspectives on Therapeutic Options for Carbapenemase-Producing Enterobacterales Infections. Microorganisms 2021; 9:730. [PMID: 33807464 PMCID: PMC8065494 DOI: 10.3390/microorganisms9040730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) are included in the list of the most threatening antibiotic resistance microorganisms, being responsible for often insurmountable therapeutic issues, especially in hospitalized patients and immunocompromised individuals and patients in intensive care units. The enzymatic resistance to carbapenems is encoded by different β-lactamases belonging to A, B or D Ambler class. Besides compromising the activity of last-resort antibiotics, CRE have spread from the clinical to the environmental sectors, in all geographic regions. The purpose of this review is to present present and future perspectives on CRE-associated infections treatment.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania; (C.O.V.); (E.G.D.); (I.B.); (M.C.C.)
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Elena Georgiana Dobre
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania; (C.O.V.); (E.G.D.); (I.B.); (M.C.C.)
| | - Irina Gheorghe
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania; (C.O.V.); (E.G.D.); (I.B.); (M.C.C.)
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Ilda Barbu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania; (C.O.V.); (E.G.D.); (I.B.); (M.C.C.)
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Roxana Elena Cristian
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania; (C.O.V.); (E.G.D.); (I.B.); (M.C.C.)
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
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28
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Fu Y, Liu W, Liu M, Zhang J, Yang M, Wang T, Qian W. In vitro anti-biofilm efficacy of sanguinarine against carbapenem-resistant Serratia marcescens. BIOFOULING 2021; 37:341-351. [PMID: 33947279 DOI: 10.1080/08927014.2021.1919649] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
Abstract
Sanguinarine, a plant-derived benzophenanthridine alkaloid, was studied in terms of its anti-biofilm effects against carbapenem-resistant Serratia marcescens (CRSM). Minimum inhibitory concentrations (MICs) and cell membrane integrity were measured to investigate the antimicrobial mechanism of sanguinarine. Additionally, the extent of biofilm formation by CRSM exposed to sanguinarine was measured by crystal violet staining and visualized via field emission scanning electron microscopy and confocal laser scanning microscopy. Sanguinarine displayed moderate activity against CRSM, with a MIC90 of 32 μg ml-1. Moreover, cell membrane integrity was severely disrupted by sanguinarine at 64 μg ml-1, and biofilm formation was sharply inhibited at 32 μg ml-1. The minimum biofilm eradication concentration was 512 μg ml-1 against mature CRSM biofilms. The overall results suggest that sanguinarine is a potential anti-biofilm agent that can be explored to treat CRSM infections.
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Affiliation(s)
- Yuting Fu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Wanting Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Miao Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Jianing Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Min Yang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Ting Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Weidong Qian
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
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29
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Serwecińska L, Kiedrzyńska E, Kiedrzyński M. A catchment-scale assessment of the sanitary condition of treated wastewater and river water based on fecal indicators and carbapenem-resistant Acinetobacter spp. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:142266. [PMID: 33182211 DOI: 10.1016/j.scitotenv.2020.142266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/22/2020] [Accepted: 09/06/2020] [Indexed: 05/14/2023]
Abstract
Urbanization and population growth have created considerable sanitation challenges in cities and communities in many parts of Europe and the world. As such, it is imperative to identify the most environmentally-harmful microbiological and chemical sources of pollution, these being wastewater treatment plants (WWTPs) which release wastewater of low quality. In the present manuscript, an extensive study was performed of the sanitary conditions of river water and treated wastewater from seventeen WWTPs of various sizes along the Pilica River catchment in central Poland, with the aim of identifying "hot spots" in terms of most serious sources of sanitary hazards. The bacteriological risk for the river, including fecal indicator bacteria (FIB) such as coliforms, E.coli, enterococci, C. perfringens, and carbapenem-resistant Acinetobacter spp. (CRA) were assessed using classical microbiological methods, and the physicochemical parameters were also tested. The WWTPs, particularly the small ones (<2000 people equivalent, PE) demonstrated significant variation regarding the physicochemical parameters. Carbapenem-resistant Acinetobacter spp. bacteria growing at 42 °C were found in the effluent wastewaters of all tested municipal WWTPs, and in most of the Pilica River water samples, presenting a potential hazard to public health. A positive correlation was identified between E. coli and CRA abundance in treated wastewater; however, no such relationship was found in river water. It was found that seven small treatment plants discharged wastewater with very different microbiological parameters. Moreover, three small treatment plants serving only 0.56% of the population in the studied area continuously released extremely high microbiological contamination, constituting as much as 54-82% of fecal indicator bacteria loads in the area studied. Our findings show that this type of comprehensive analysis may enable assessment of the use of the entire catchment area, thus identifying the most serious threats to surface water quality and guiding the actions needed to improve the worst operating WWTPs.
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Affiliation(s)
- Liliana Serwecińska
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90-364 Lodz, Poland
| | - Edyta Kiedrzyńska
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90-364 Lodz, Poland; UNESCO Chair on Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland.
| | - Marcin Kiedrzyński
- Department of Geobotany and Plant Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha12/16, 90-237 Lodz, Poland
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Lü Y, Kang H, Fan J. A Novel bla CTX-M-65-Harboring IncHI2 Plasmid pE648CTX-M-65 Isolated from a Clinical Extensively-Drug-Resistant Escherichia coli ST648. Infect Drug Resist 2020; 13:3383-3391. [PMID: 33061485 PMCID: PMC7533269 DOI: 10.2147/idr.s269766] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Background An ESBL, carbapenemase- and MCR-1-producing Escherichia coli ST648 strain was isolated from the urine sample of a patient in a Chinese tertiary hospital in 2016. Methods The strain was fully sequenced by GridION X5 platform of Oxford Nanopore Technology. Results The sequence analysis showed that the extended-spectrum β-lactamases CTX-M-65 and OXA-1, the carbapenemase NDM-5, the MCR-1 were encoded, respectively, by three different resistance plasmids. The pE648CTX-M-65-carrying blaCTX-M-65 was a novel conjugative plasmid belonging to IncHI2 type; except for the blaCTX-M-65, it also carried resistance genes ble, floR, sul1, aph(4)-Ia, aac(3)-VI, aac(6ʹ)-II, blaOXA-1, catB, arr3 and tetA. Besides, an IncX4 plasmid pE648MCR-1-carrying mcr-1 and an IncX3 plasmid pE648NDM-5-carrying blaNDM-5 were also identified. Conclusion The three transferable resistance plasmids coexisting in the E. coli ST648 isolate indicated the high risk to disseminate the extensively-drug-resistance among Enterobacteriaceae.
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Affiliation(s)
- Yang Lü
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Haiquan Kang
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, People's Republic of China
| | - Jianming Fan
- The Laboratory of Toxicology, College of Public Health, Zhengzhou University, Zhengzhou 450001, People's Republic of China
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Su S, Li C, Zhao Y, Yu L, Wang Y, Wang Y, Bao M, Fu Y, Zhang J, Zhang X. Outbreak of KPC-2–Producing Klebsiella pneumoniae ST76 Isolates in an Intensive Care Unit and Neurosurgery Unit. Microb Drug Resist 2020; 26:1009-1018. [PMID: 32150494 DOI: 10.1089/mdr.2019.0363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Shanshan Su
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Microbiology, The First People's Hospital of Jingzhou City, Jingzhou, China
| | - Chunjiang Li
- Department of Microbiology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Yongxin Zhao
- Department of Microbiology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Lan Yu
- Department of Microbiology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Yong Wang
- Department of Microbiology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Yuchao Wang
- Department of Microbiology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Mingjia Bao
- Center for Disease Control and Prevention, Jiamusi, China
| | - Yu Fu
- Center for Disease Control and Prevention, Jiamusi, China
| | - Jisheng Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Microbiology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Xiaoli Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Microbiology, First Affiliated Hospital of Jiamusi University, Jiamusi, China
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Cai Z, Tao J, Jia T, Fu H, Zhang X, Zhao M, Du H, Yu H, Shan B, Huang B, Chen L, Tang YW, Jia W, Qu F. Multicenter Evaluation of the Xpert Carba-R Assay for Detection and Identification of Carbapenemase Genes in Sputum Specimens. J Clin Microbiol 2020; 58:e00644-20. [PMID: 32522829 PMCID: PMC7448655 DOI: 10.1128/jcm.00644-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
Rapid diagnosis of infections caused by carbapenem-resistant Enterobacteriaceae (CRE) is crucial for proper treatment and infection control. The Xpert Carba-R assay is a qualitative multiplex real-time PCR method that qualitatively detects and differentiates five common carbapenemase genes (blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP) directly from rectal swabs or purified colonies within approximately 1 h. We performed a multicenter evaluation of the investigational use of the Carba-R assay for detection and differentiation of carbapenemase genes from sputum specimens in patients with a clinical diagnosis of pneumonia. The intra- and interassay coefficients of variation values for the Carba-R assay were 0.2% to 2.0% and 1.4% to 2.3%, respectively. A total of 301 sputum specimens were collected and tested. Compared to bacterial culture followed by PCR identification of resistance genes from colonies, the Carba-R assay reduced turnaround time from 56 to 84 h to less than 2 h. Carbapenemase genes were detected by the Carba-R assay in Klebsiella pneumoniae (n = 236), Escherichia coli (n = 22), Enterobacter cloacae (n = 23), Klebsiella oxytoca (n = 8), Serratia marcescens (n = 6), Citrobacter freundii (n = 4), and Klebsiella aerogenes (n = 2). The Carba-R assay detected 112 blaKPC (33.5%), 70 blaNDM (21.0%), 8 blaIMP (2.4%), and 2 blaVIM (0.6%) genes, with positive percent agreement, negative percent agreement, and concordance rates of 92.9%, 86.7%, and 88.3%, respectively, for the dominant blaKPC and 85.0%, 87.8%, and 87.4%, respectively, for the blaNDM genes. Neither method detected the blaOXA-48 carbapenemase gene. The convenient, rapid, and simple characteristics of the Xpert Carba-R assay make it a potential tool for CRE detection and identification directly in sputum specimens.
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Affiliation(s)
- Zhen Cai
- China Aviation General Hospital of China Medical University, Beijing, China
| | - Jia Tao
- Center of Medical Laboratory, the General Hospital of Ningxia Medical University, Yinchuan, China
| | - Tianye Jia
- The Center of Clinical Diagnosis Laboratory, 302 Hospital of PLA, Beijing, China
| | - Hongyu Fu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xin Zhang
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mei Zhao
- Center of Medical Laboratory, the General Hospital of Ningxia Medical University, Yinchuan, China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Hua Yu
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Bin Shan
- Department of Laboratory Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liang Chen
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Seton Hall University, Nutley, New Jersey, USA
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
- Cepheid, Shanghai, China
| | - Wei Jia
- Center of Medical Laboratory, the General Hospital of Ningxia Medical University, Yinchuan, China
| | - Fen Qu
- China Aviation General Hospital of China Medical University, Beijing, China
- The Center of Clinical Diagnosis Laboratory, 302 Hospital of PLA, Beijing, China
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Jiang B, Du P, Jia P, Liu E, Kudinha T, Zhang H, Li D, Xu Y, Xie L, Yang Q. Antimicrobial Susceptibility and Virulence of mcr-1-Positive Enterobacteriaceae in China, a Multicenter Longitudinal Epidemiological Study. Front Microbiol 2020; 11:1611. [PMID: 32849334 PMCID: PMC7399235 DOI: 10.3389/fmicb.2020.01611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/19/2020] [Indexed: 11/26/2022] Open
Abstract
This study was to investigate the prevalence of mcr-1-positive Enterobacteriaceae (MPE) in intra-abdominal infections (IAIs), urinary tract infections (UTIs), and lower respiratory tract infections (LRTIs) in China. A total of 6,401 Enterobacteriaceae isolates were collected consecutively from IAI, UTI, and LRTI patients in 19 hospitals across mainland China during 2014–2016. MPE isolates were screened by PCR detection for the mcr gene. The resistance profiles were tested by antimicrobial susceptibility test. All MPE isolates were characterized by pulsed-field gel electrophoresis (PFGE), multi-locus-sequence typing, O and H serotyping, and whole-genome sequencing. Among the 6,401 Enterobacteriaceae isolates, 17 Escherichia coli strains (0.27%) were positive for the mcr-1 gene. The MPE prevalence rates in IAI, UTI, and LRTI patients were 0.34% (12/3502), 0.23% (5/2154), and 0% (0/745), respectively. The minimum inhibition concentrations (MICs) of colistin against 3 isolates were of 0.5–2 mg/L, and 4–8 mg/L against other 14 isolates. All the 17 isolates were susceptible to meropenem, imipenem, tigecycline, and ceftazidime/avibactam. The 17 MPE isolates belonged to 14 different ST types, and those that belonged to the same STs were not clonal by PFGE. The mcr-1-harboring plasmid of ten MPE isolates could transfer to the recipients by conjugation and the colistin MICs of the transconjugants ranged from 0.5 to 8 mg/L. Mcr-1-carrying plasmids from the 17 MPE isolates could be grouped into four clusters, including 8 IncX4 type, 4 IncI2 type, 4 IncHI2A type, and 1 p0111 type. Multiple-drug resistance genes and virulence genes were detected. In conclusion, the prevalence of MPE in IAI, UTI, and LRTI were low in China, and no clonal transmission was identified in our study. Most MPE isolates exhibited low-level colistin resistance. However, our study indicated that MPE isolates always carried a variety of drug resistance and virulence genes, which should be paid more attention.
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Affiliation(s)
- Bin Jiang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Department of Clinical Laboratory, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Pengcheng Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Peiyao Jia
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Enbo Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Orange, NSW, Australia
| | - Hui Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Dongxue Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Liangyi Xie
- Department of Clinical Laboratory, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Jin C, Zhou F, Cui Q, Qiang J, An C. Molecular Characteristics of Carbapenem-Resistant Enterobacter cloacae in a Tertiary Hospital in China. Infect Drug Resist 2020; 13:1575-1581. [PMID: 32547127 PMCID: PMC7266308 DOI: 10.2147/idr.s254056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Background Infections caused by the carbapenem-resistant Enterobacter cloacae (CREC) bring great challenges to the clinical treatment and pose a serious threat to public health. In this study, we investigated the molecular characteristics of CREC in a tertiary hospital. Materials and Methods A total of 12 non-duplicate CREC strains isolated during the period of November 2016 to July 2019 were subjected to automated microbial identification and antimicrobial susceptibility testing (AST) using the BD Phoenix-100 identification and antimicrobial susceptibility testing (ID/AST) system. The strains were also subjected to phenotypic screening for the detection of antibiotic resistance genes such as the carbapenemase and other β-lactamase genes, with the use of the polymerase chain reaction assay (PCR). Finally, multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE)-based homology analysis were applied. Results Four types of carbapenemases namely IMP-26, NDM-5, NDM-1, and KPC-2 were identified in 12 CREC strains. IMP-26 was the most prevalent type (6/12 strains, 50 %), followed by NDM-5 (3/12 strains, 25 %). The results of MLST revealed that these 12 strains could be divided into five sequence types (STs) among which ST544 was the dominant type (6/12 strains, 50 %). The PFGE results divided the 12 strains into four clusters. Conclusion Our study indicated that the epidemics of the IMP-26-producing E. cloacae ST544 strain did occur in the intensive care unit (ICU) of a tertiary hospital. Therefore, early surveillance and strict implementation of control measures are crucial for the prevention of nosocomial infections and transmissions in hospitals.
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Affiliation(s)
- Chunmei Jin
- Department of Clinical Laboratory, Yanbian University Hospital, Yanji, People's Republic of China
| | - Fuxian Zhou
- Department of Clinical Laboratory, Yanbian University Hospital, Yanji, People's Republic of China
| | - Qingsong Cui
- Department of Intensive Care Unit, Yanbian University Hospital, Yanji, People's Republic of China
| | - Jixiang Qiang
- Department of Clinical Laboratory, Yanbian University Hospital, Yanji, People's Republic of China
| | - Changshan An
- Department of Respiratory Medicine, Yanbian University Hospital, Yanji, People's Republic of China
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Zou H, Berglund B, Xu H, Chi X, Zhao Q, Zhou Z, Xia H, Li X, Zheng B. Genetic characterization and virulence of a carbapenem-resistant Raoultella ornithinolytica isolated from well water carrying a novel megaplasmid containing bla NDM-1. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:114041. [PMID: 32006889 DOI: 10.1016/j.envpol.2020.114041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/31/2019] [Accepted: 01/21/2020] [Indexed: 05/16/2023]
Abstract
Infections caused by carbapenem-resistant Enterobacteriaceae are a growing concern worldwide. Raoultella ornithinolytica is a species in the Enterobacteriaceae family which can cause hospital-acquired infections and is sporadically reported as carbapenem-resistant from human and environmental sources. In this study, we firstly report on an NDM-1-producing R. ornithinolytica, Rao166, isolated from drinking water in an animal cultivation area in China. In addition to carbapenem-resistance, Rao166 was resistant to several other antibiotics including gentamicin, sulfamethoxazole-trimethoprim, tetracycline and fosfomycin. Rao166 carried a novel IncFIC-type megaplasmid, 382,325 bp in length (pRAO166a). A multidrug resistance region, 60,600 bp in length, was identified in the plasmid containing an aac(3)-IId-like gene, aac(6')-Ib-cr, blaDHA-1, blaTEM-1B, blaCTX-M-3, blaOXA-1, blaNDM-1, qnrB4, catB3, arr-3, sul1, and tet(D). Results from virulence assays implied that Rao166 has considerable pathogenic potential. Although pRAO166a was found to be non-transmissible, dissemination of the NDM-1 producing strain may occur from well water to humans or animals through cross-contamination during food preparation or directly via drinking water, and potentially lead to difficult-to-treat infections. Thus, contamination of well water by this carbapenem-resistant and presumptively virulent strain of R. ornithinolytica should be considered a potential public health risk.
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Affiliation(s)
- Huiyun Zou
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, 250012, China
| | - Björn Berglund
- Department of Clinical and Experimental Medicine, Linköping University, 581 85, Linköping, Sweden; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohui Chi
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, 250012, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qian Zhao
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, 250012, China
| | - Ziyu Zhou
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, 250012, China
| | - Huiyu Xia
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, 250012, China
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, 250012, China.
| | - Beiwen Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Li Y, Huang J, Wang X, Xu C, Han T, Guo X. Genetic Characterization of the O-Antigen and Development of a Molecular Serotyping Scheme for Enterobacter cloacae. Front Microbiol 2020; 11:727. [PMID: 32411106 PMCID: PMC7198725 DOI: 10.3389/fmicb.2020.00727] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/27/2020] [Indexed: 11/13/2022] Open
Abstract
Enterobacter cloacae is a well-characterized opportunistic pathogen that is closely associated with various nosocomial infections. The O-antigen, which is one of the most variable constituents on the cell surface, has been used widely and traditionally for serological classification of many gram-negative bacteria. E. cloacae is divided into 30 serotypes, based on its O-antigen diversity. In this study, by using genomic and comparative-genomic approaches, we analyzed the O-antigen gene clusters of 26 E. cloacae serotypes in depth. We also identified the sero-specific gene for each serotype and developed a multiplex polymerase chain reaction (PCR) method. The sensitivity of the assay was 0.1 ng for genomic DNA and 103 colony forming units for pure cultures. The assay reliability was evaluated by double-blinded testing with 81 clinical strains. Furthermore, we established a valid, genome-based tool for in silico serotyping of E. cloacae. By screening 431 E. cloacae genomes deposited in GenBank, 304 were classified into current antigenic scheme, and 112 were allocated into 55 putative novel serotypes. Our results represent the first genetic basis of the O-antigen diversity and variation of E. cloacae, providing a rationale for studying the O-antigen associated evolution and pathogenesis of this bacterium. In addition, we extended the current serotyping system for E. cloacae, which is important for detection and epidemiological surveillance purposes for this important pathogen.
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Affiliation(s)
- Yayue Li
- The Third Central Hospital of Tianjin, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Junjie Huang
- Department of Vascular Surgery, Tianjin Hospital, Tianjin, China
| | - Xiaotong Wang
- Tianjin Children's Hospital, Third Central Clinical College of Tianjin Medical University, Tianjin, China
| | - Cong Xu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Tao Han
- The Third Central Hospital of Tianjin, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Xi Guo
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
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Xu Q, Fu Y, Zhao F, Jiang Y, Yu Y. Molecular Characterization of Carbapenem-Resistant Serratia marcescens Clinical Isolates in a Tertiary Hospital in Hangzhou, China. Infect Drug Resist 2020; 13:999-1008. [PMID: 32308441 PMCID: PMC7152788 DOI: 10.2147/idr.s243197] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Introduction Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most commonly associated with clinical infections, data on Serratia marcescens are inadequate and superficial. Methods In this study, we characterized 36 carbapenem-resistant Serratia marcescens (CRSM) isolates in our hospital from April 2018 to March 2019 by analysing whole-genome sequencing (WGS) data. The molecular typing of the isolates was performed using both pulsed-field gel electrophoresis (PFGE) and core genome multilocus sequence typing (cgMLST). Results Thirty-three of the 36 isolates showed carbapenem resistance conferred by a blaKPC-2-harbouring plasmid, while the remaining three isolates were characterized by overexpression of beta-lactamase combined with porin loss. The blaKPC-2 genes in all the isolates were located on a plasmid of ~103 kb, except one, which was on a plasmid of ~94 kb. The gene structure surrounding blaKPC-2 in the plasmids was confirmed by integration of a partial Tn4401 structure and an intact IS26 as previously reported. Most of the plasmids also contained a mobile genetic element (MGE) comprising qnr and ISKpn19, which provided evidence of horizontal transfer of antibiotic resistance genes. Conclusion The thirty-six CRSM isolates were mainly clonally disseminated with a blaKPC-2-harbouring plasmid in our hospital. The gene structure surrounding blaKPC-2 as an MGE, as well as the qnr segment, might be acquired by horizontal gene transfer, and it could aggravate the infection and increase the difficulty of clinical treatment.
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Affiliation(s)
- Qian Xu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou City, Zhejiang Province, 310016, People's Republic of China
| | - Ying Fu
- Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou City, Zhejiang Province 310016, People's Republic of China
| | - Feng Zhao
- Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou City, Zhejiang Province 310016, People's Republic of China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou City, Zhejiang Province, 310016, People's Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou City, Zhejiang Province, 310016, People's Republic of China
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Zhao Y, Zhang S, Fang R, Wu Q, Li J, Zhang Y, Rocker A, Cao J, Lithgow T, Zhou T. Dynamic Epidemiology and Virulence Characteristics of Carbapenem-Resistant Klebsiella pneumoniae in Wenzhou, China from 2003 to 2016. Infect Drug Resist 2020; 13:931-940. [PMID: 32280249 PMCID: PMC7128075 DOI: 10.2147/idr.s243032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/03/2020] [Indexed: 12/28/2022] Open
Abstract
Purpose To investigate transitions in resistance mechanisms, virulence characteristics and molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae (CRKP) during 2003–2016 in a major Eastern Chinese medical center. Patients and Methods From a total of 2299 K. pneumoniae clinical strains collected from 2003 to 2016, 214 were found to be CRKP isolates and were selected for further study. Characterization of these was conducted by molecular detection of antibiotic resistance markers and virulence determinants, modified carbapenem inactivation method and multilocus sequence typing (MLST). Results In this study, the prevalence of CRKP was increasing over the 14-year period, mirroring a national trend. These CRKP strains were resistant to most of the tested, clinically relevant drugs. The majority of these CRKP strains were positive for carbapenemases, with the Klebsiella pneumoniae carbapenemase (KPC) found to be the dominant type (207/210, 98.6%). The carrier rates of virulence genes uge, entB, fimH, mrkD and ureA increased in 2016, while the ybtA, iucA and irp2 showed a relatively constant trend. From MLST data, ST11 (88.8%, 190/214) was the preponderant sequence type (ST), followed by ST15 (1.9%, 4/214) and ST656 (1.4%, 3/214). Several strains with less common STs (ST690, ST895, ST1823 and ST1384) were also detected, and these too showed high levels of antimicrobial resistance. Conclusion The average national rise in CRKP across China is mirrored in this in-depth analysis of a single hospital, while the prevalence of hypervirulent CRKP (such as ST15) was relatively low as of 2016. Continuous monitoring is necessary to keep track of CRKP and should include the prospect of newly emerging strains with less common STs and the prospect of detecting carbapenem-resistant, carbapenemase-negative Klebsiella pneumoniae.
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Affiliation(s)
- Yajie Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Siqin Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Renchi Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Qing Wu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Jiahui Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Yizhi Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Andrea Rocker
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Jianming Cao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
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Alsharapy SA, Gharout-Sait A, Muggeo A, Guillard T, Cholley P, Brasme L, Bertrand X, Moghram GS, Touati A, De Champs C. Characterization of Carbapenem-Resistant Enterobacteriaceae Clinical Isolates in Al Thawra University Hospital, Sana'a, Yemen. Microb Drug Resist 2020; 26:211-217. [DOI: 10.1089/mdr.2018.0443] [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)
- Sameer Ahmed Alsharapy
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
- Department of Microbiology, Al Thawra University Hospital, Sana'a, Yemen
| | - Alima Gharout-Sait
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Anaelle Muggeo
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière, CHU Reims, Hôpital Robert DEBRE, Reims, France
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, Reims, France
| | - Thomas Guillard
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière, CHU Reims, Hôpital Robert DEBRE, Reims, France
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, Reims, France
| | - Pascal Cholley
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
- UMR CNRS 6249, Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Lucien Brasme
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière, CHU Reims, Hôpital Robert DEBRE, Reims, France
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, Reims, France
| | - Xavier Bertrand
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
- UMR CNRS 6249, Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | | | - Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Christophe De Champs
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière, CHU Reims, Hôpital Robert DEBRE, Reims, France
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, Reims, France
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40
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Tian X, Huang C, Ye X, Jiang H, Zhang R, Hu X, Xu D. Carbapenem-Resistant Enterobacter cloacae Causing Nosocomial Infections in Southwestern China: Molecular Epidemiology, Risk Factors, and Predictors of Mortality. Infect Drug Resist 2020; 13:129-137. [PMID: 32021327 PMCID: PMC6959490 DOI: 10.2147/idr.s234678] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/13/2019] [Indexed: 11/23/2022] Open
Abstract
Background The emergence and spread of carbapenem-resistant Enterobacter cloacae (CR-ECL) have posed a serious threat to clinical management. This retrospective study assessed the epidemiological characteristics of CR-ECL to explore the risk factors and predictors of mortality in patients with CR-ECL infection. Methods We performed a retrospective 1:2 case-control study of hospitalized patients from January 2014 to December 2017. A total of 85 consecutive unique CR-ECL strains comprised the case group, and 170 matched patients with carbapenem-susceptible Enterobacter cloacae (CS-ECL) infection at the same period as the control group. Isolates were screened for potential resistance genes by polymerase chain reaction (PCR) and molecular typing was performed by multilocus sequence typing (MLST). Results The results of drug resistance gene detection showed that blaNDM-1 was the most common carbapenem resistance gene. The MLST results showed that ST51 was the predominant epidemic type, followed by ST88. ICU admission (P<0.001), drainage tube (P=0.002), central venous catheter (P=0.005), and carbapenem exposure (P=0.003) were independent risk factors for CR-ECL infection. Significant predictors for 28-day mortality included solid tumours (P=0.005), septic shock (P=0.019), and mechanical ventilation (P=0.027). Conclusion Our study indicated that ST51 and ST88, which are closely related, were the predominant epidemic types of CR-ECL producing blaNDM-1 in southwestern China. Strengthening the surveillance of patients with solid tumours, septic shock and mechanical ventilation is an urgent need.
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Affiliation(s)
- Xiaolang Tian
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Changwu Huang
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Xiaoli Ye
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Hongyan Jiang
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Rufang Zhang
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Xiaofang Hu
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Dongshuang Xu
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
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41
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Hu W, Li M, Lu W, Guo S, Li J. Evaluation of MASTDISCS combi Carba plus for the identification of metallo-β-lactamases, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae clinical isolates. Lett Appl Microbiol 2019; 70:42-47. [PMID: 31642085 DOI: 10.1111/lam.13240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/07/2019] [Accepted: 10/21/2019] [Indexed: 11/30/2022]
Abstract
The increasing frequency of class A KPC enzymes, class B metallo-β-lactamases (MBLs) and class D OXA-48 enzymes in Enterobacteriaceae makes their early identification urgent. A simple commercial MASTDISCS combi Carba plus disc system (MAST-Carba plus) was designed for the identification of MBLs, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae. To validate the MAST-Carba plus, a total of 77 isolates of carbapenemase-producing Enterobacteriaceae (CPE) and 84 isolates of noncarbapenemase-producing Enterobacteriaceae (non-CPE) were selected for differentiation of the genes of Enterobacteriaceae by MAST-Carba plus. Meanwhile, the carbapenemase genes such as blaKPC , blaIMP , blaVIM , blaNDM-1 and blaOXA-48 were detected by PCR (polymerase chain reaction). Thus, when considered on the basis of PCR results, the sensitivity of MAST-Carba plus detection of KPC strains is 82·3%, the specificity is 100·0%, the positive predictive value is 100·0% and the negative predictive value is 92·4%. For MBLs strains, the sensitivity is 100·0%, the specificity is 97·1%, the positive predictive value is 84·6% and the negative predictive value is 100·0%. For OXA-48 strains, the sensitivity is 100·0%, the specificity is 99·4%, the positive predictive value is 80·0% and the negative predictive value is 100·0%. Our findings suggest that MAST-Carba plus is a rapid and promising method for identifying the MBLs, KPC and OXA-48 carbapenemase genes in Enterobacteriaceae, which could be exploited in basic microbiology laboratory to prevent the transmission of CPE. SIGNIFICANCE AND IMPACT OF THE STUDY: Not only detection of carbapenemases but also identification of their genes accurately and rapidly in Enterobacteriaceae is still a major challenge for clinical laboratories in order to prevent the transmission of carbapenemase-producing Enterobacteriaceae (CPE). Therefore, this study aimed to evaluate the performance of a new rapid method (MASTDISCS combi Carba plus) for the identification of metallo-β-lactamases (MBLs), KPC and OXA-48 carbapenemase genes in Enterobacteriaceae clinical isolates.
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Affiliation(s)
- W Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - M Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - W Lu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - S Guo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - J Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
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42
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Wang S, Xu L, Chi X, Li Y, Kou Z, Hou P, Xie H, Bi Z, Zheng B. Emergence of NDM-1- and CTX-M-3-Producing Raoultella ornithinolytica in Human Gut Microbiota. Front Microbiol 2019; 10:2678. [PMID: 31824461 PMCID: PMC6883284 DOI: 10.3389/fmicb.2019.02678] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/05/2019] [Indexed: 12/21/2022] Open
Abstract
Raoultella ornithinolytica is an opportunistic pathogen of the Enterobacteriaceae family and has been implicated in nosocomial infections in recent years. The aim of this study was to characterize a carbapenemase-producing R. ornithinolytica isolate and three extended-spectrum β-lactamase (ESBL)-producing R. ornithinolytica isolates from stool samples of adults in a rural area of Shandong Province, China. The species were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequence analysis. Antimicrobial susceptibility test showed that all four isolates were multidrug-resistant (MDR). The whole genome sequence (WGS) of these isolates was determined using an Illumina HiSeq platform, which revealed MDR-related genes. The S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE) was used to characterize the plasmids carried by the R. ornithinolytica isolates. The blaNDM-1 and blaCTX-M-3 genes were probed using Southern blotting, which confirmed the location of both genes on the same plasmid with molecular weight of 336.5–398.4 kb. The transferability of blaNDM-1 and blaCTX-M was also confirmed by conjugation assays. Finally, BLAST analysis of both genes showed that mobile genetic elements were associated with the spread of drug resistance genes. Taken together, we report the presence of conjugative blaNDM-1 and blaCTX-M plasmids in R. ornithinolytica isolates from healthy humans, which indicate the possibility of inter-species transfer of drug resistance genes. To the best of our knowledge, this is the first study to isolate and characterize carbapenemase-producing R. ornithinolytica and ESBL-producing R. ornithinolytica isolates from healthy human hosts.
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Affiliation(s)
- Shuang Wang
- Bacterial Infection Disease Control of Institute, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Liuchen Xu
- Bacterial Infection Disease Control of Institute, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Xiaohui Chi
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Yan Li
- Bacterial Infection Disease Control of Institute, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Zengqiang Kou
- Bacterial Infection Disease Control of Institute, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Peibin Hou
- Bacterial Infection Disease Control of Institute, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Hengjie Xie
- Department of Supervise Sampling, Shandong Institute for Food and Drug Control, Jinan, China
| | - Zhenwang Bi
- Bacterial Infection Disease Control of Institute, Shandong Center for Disease Control and Prevention, Jinan, China.,Shandong Academy of Clinical Medicine, Shandong Provincial Hospital, Jinan, China
| | - Beiwen Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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