1
|
Shelenkov A, Akimkin V, Mikhaylova Y. International Clones of High Risk of Acinetobacter Baumannii-Definitions, History, Properties and Perspectives. Microorganisms 2023; 11:2115. [PMID: 37630675 PMCID: PMC10459012 DOI: 10.3390/microorganisms11082115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/24/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of A. baumannii is driven by several lineages named 'international clones of high risk' (ICs), two of which were first revealed in the 1970s. Epidemiological surveillance is a crucial tool for controlling the spread of this pathogen, which currently increasingly involves whole genome sequencing. However, the assignment of a particular A. baumannii isolate to some IC based on its genomic sequence is not always straightforward and requires some computational skills from researchers, while the definitions found in the literature are sometimes controversial. In this review, we will focus on A. baumannii typing tools suitable for IC determination, provide data to easily determine IC assignment based on MLST sequence type (ST) and intrinsic blaOXA-51-like gene variants, discuss the history and current spread data of nine known ICs, IC1-IC9, and investigate the representation of ICs in public databases. MLST and cgMLST profiles, as well as OXA-51-like presence data are provided for all isolates available in GenBank. The possible emergence of a novel A. baumannii international clone, IC10, will be discussed.
Collapse
Affiliation(s)
- Andrey Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | | | | |
Collapse
|
2
|
Abrahams I, Dramowski A, Moloto K, Lloyd L, Whitelaw A, Bekker A. Colistin use in a carbapenem-resistant Enterobacterales outbreak at a South African neonatal unit. S Afr J Infect Dis 2023; 38:487. [PMID: 36756243 PMCID: PMC9900379 DOI: 10.4102/sajid.v38i1.487] [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: 09/27/2022] [Accepted: 12/05/2022] [Indexed: 02/04/2023] Open
Abstract
Background Colistin is increasingly prescribed for neonates with carbapenem-resistant Enterobacterales (CRE) infections. Objectives We described patient demographics, infection episodes, treatment and clinical outcomes, colistin related adverse events and relatedness of isolates in neonates with clinically confirmed or clinically suspected CRE infections. Method The authors retrospectively reviewed culture-confirmed and clinically suspected culture-negative CRE infections at a South African neonatal unit during a CRE outbreak. Results Fifty-three neonates (median gestational age 29 weeks and birth weight 1185 g) were included. Twenty-three of 53 neonates (43%) had culture-confirmed CRE (17 received colistin; 6 died without receiving colistin) and 30 (57%) received colistin for clinically suspected CRE infection but were ultimately culture-negative. Prior respiratory support and surgical conditions were present in 37/53 (70%) and 19/53 (36%) neonates, respectively. Crude mortality was high (20/53; 38%) with no significant difference between culture-confirmed CRE versus clinically suspected culture-negative CRE groups (10/23 [44%] vs 10/30 [33%]; p = 0.45). Hypomagnesaemia (10/38; 26%) and hypokalaemia (15/38; 40%) were frequent; acute kidney injury was rare (1/44; 2%). Three CRE infection clusters were identified by genotypic analysis of 20 available isolates (18 [90%] bla NDM-1 [New Delhi metallo-beta-lactamase], 2 [10%] bla OXA [oxacillinase]-48). Conclusion Neonates receiving colistin therapy were predominantly preterm, with multiple risk factors for infection. Colistin-associated electrolyte derangement was frequent. Over one-third of neonates died. Bla NDM-1 was the most frequent carbapenemase gene identified in the outbreak isolates. Contribution Colistin was safely used during an Enterobacterales outbreak in predominantly premature and surgical neonates. The mortality was high.
Collapse
Affiliation(s)
- Ilhaam Abrahams
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kedisaletse Moloto
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Lizel Lloyd
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Adrie Bekker
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| |
Collapse
|
3
|
Hussain MI, Borah P, Hussain I, Sharma RK, Kalita MC. Densitometric analysis of rep-PCR data: Insight into genetic variability and transmission of Clostridium perfringens typed with an improved multiplex PCR. Anaerobe 2021; 70:102383. [PMID: 34089857 DOI: 10.1016/j.anaerobe.2021.102383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 11/15/2022]
Abstract
An epidemiological study was conducted in North-East India (part of Indo-Burma biodiversity hotspot) to better understand the distribution, diversity, and transmission of Clostridium perfringens among livestock, pets, wild animals (captive), and humans. A total of 160 C. perfringens isolates were recovered from 642 diarrhoeic faecal samples with an isolation rate of 24.92%. Isolation rate was the highest among captive wild animals (37.5%) followed by dog (34.6%), human (33.8%), pig (32.7%), cattle (20.8%), goat (18.3%) and poultry (9.3%). Isolates were toxin typed using a seven gene multiplex PCR designed for simultaneous detection of cpa, cpb, cpb2, etx, iap, cpe and netB. The majority of isolates, 128 (80%) were of type A, followed by 17 (10.62%), 5 (3.12%), 4 (2.5%), 3 (1.87%), 2 (1.25%) and 1 (0.63%) isolates of type C, D, E, G, F and B, respectively. Beta 2 toxin gene was present in 65 (50%) of type A isolates, followed by 7 (41.2%), 4 (80%), 1(25%), and 1 (100%) of type C, D, G and B isolates, respectively. Beta 2 toxin has a high prevalence among dogs (28.6%), cattle (27.3%), and pig (20.8%) compared to humans, goat, wild animals, and poultry (1.2-14.3%). The prevalence of CPE and NetB toxin-positive strains was low, with only 3 (1.8%) and 5 (3.1%) isolates, respectively. Association of C. perfringens with diarrhoea in Civet Cat, Golden Langur, and Gray Langur has been reported for the first time. The genetic diversity and transmission of isolates were investigated using automated rep-PCR (Diversilab®, bioMérieux) using two densitometry-based matrices: modified Kullback-Leibler (KL) and Pearson's correlation (PC). The PC and modified KL matrices formed three distinct clusters with 59% and 27.2% similarity, respectively. C. perfringens diversity and transmission were best studied using modified KL matrix that placed more emphasis on the presence of bands rather than intensity. However, the PC method was found to be more suitable for differentiating strains within a toxin type, with slightly higher D-values.
Collapse
Affiliation(s)
- Md Iftikar Hussain
- Department of Bioengineering and Technology, Gauhati University, Assam, 781014, India.
| | - Probodh Borah
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Assam, 781022, India; Advanced State Biotech Hub (Assam), College of Veterinary Science, Assam Agricultural University, Assam, 781022, India.
| | - Isfaqul Hussain
- Division of Veterinary Microbiology and Immunology, FVSc and AH, SKUAST-Kashmir, J&K, 190006, India.
| | - Rajeev Kumar Sharma
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Assam, 781022, India.
| | | |
Collapse
|
4
|
Snyman Y, Whitelaw AC, Reuter S, Maloba MRB, Newton-Foot M. Colistin Resistance Mechanisms in Clinical Escherichia coli and Klebsiella spp. Isolates from the Western Cape of South Africa. Microb Drug Resist 2021; 27:1249-1258. [PMID: 33571049 DOI: 10.1089/mdr.2020.0479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Objectives: Colistin is a last-resort antibiotic for the treatment of carbapenem-resistant Gram-negative infections. Colistin resistance thus poses a threat to human health. Colistin resistance is most commonly encoded by mutations in chromosomal pmrA, pmrB, phoP, phoQ, ccrB, and mgrB genes, and the presence of plasmid-mediated mcr genes. This study describes colistin resistance mechanisms in clinical Enterobacterales isolates from the Western Cape, South Africa. Results: Escherichia coli (n = 22) and Klebsiella spp. (n = 7) isolates, from nine health care facilities, were confirmed to be colistin resistant during 2016 and 2017. mcr-1 was present in 55% (12/22) of E. coli and 71% (5/7) of Klebsiella spp. isolates. Colistin resistance mutations in pmrB were identified in 8/10 mcr-negative E. coli isolates using whole-genome sequencing, with pmrB Pro-94→Gln being the most frequent with presence in 4 isolates. One mcr-negative Klebsiella spp. isolate had a complete deletion of the mgrB and one contained an insertion sequence (IS1) in mgrB. Conclusion: A reduction in the proportion of colistin-resistant isolates harboring mcr-1 from 2016 to 2017 was observed. Colistin-resistant E. coli attributed by chromosomal mutations in pmrB in 2017 were mostly clonal related, which contrasts with the 2016 unrelated mcr-1-positive isolates. The diverse strains, hospitals, and resistance mechanisms may suggest that selective pressure is the main driver of colistin resistance.
Collapse
Affiliation(s)
- Yolandi Snyman
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Cape Town, South Africa
| | - Andrew Christopher Whitelaw
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center University of Freiburg, Freiburg, Germany
| | - Motlatji Reratilwe Bonnie Maloba
- Department of Medical Microbiology, University of the Free State, Bloemfontein, South Africa.,National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Mae Newton-Foot
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| |
Collapse
|
5
|
Hwang SM, Cho HW, Kim TY, Park JS, Jung J, Song KH, Lee H, Kim ES, Kim HB, Park KU. Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii. Diagnostics (Basel) 2021; 11:diagnostics11020201. [PMID: 33573077 PMCID: PMC7910894 DOI: 10.3390/diagnostics11020201] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/16/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.
Collapse
Affiliation(s)
- Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.M.H.); (J.S.P.)
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
| | - Hee Won Cho
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Seoul 06351, Korea;
| | - Jeong Su Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.M.H.); (J.S.P.)
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
| | - Jongtak Jung
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Kyoung-Ho Song
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Hyunju Lee
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Eu Suk Kim
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Hong Bin Kim
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.M.H.); (J.S.P.)
- College of Medicine, Seoul National University, Seoul 03080, Korea; (H.W.C.); (J.J.); (K.-H.S.); (H.L.); (E.S.K.); (H.B.K.)
- Correspondence: ; Tel.: +82-2740-8005
| |
Collapse
|
6
|
de Sales RO, Migliorini LB, Puga R, Kocsis B, Severino P. A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa. Front Microbiol 2020; 11:1049. [PMID: 32528447 PMCID: PMC7264379 DOI: 10.3389/fmicb.2020.01049] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous microorganism and an important opportunistic pathogen responsible for a broad spectrum of infections mainly in immunosuppressed and critically ill patients. Molecular investigations traditionally rely on pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). In this work we propose a core genome multilocus sequence typing (cgMLST) scheme for P. aeruginosa, a methodology that combines traditional MLST principles with whole genome sequencing data. All publicly available complete P. aeruginosa genomes, representing the diversity of this species, were used to establish a cgMLST scheme targeting 2,653 genes. The scheme was then tested using genomes available at contig, chromosome and scaffold levels. The proposed cgMLST scheme for P. aeruginosa typed over 99% (2,314/2,325) of the genomes available for this study considering at least 95% of the cgMLST target genes present. The absence of a certain number gene targets at the threshold considered for both the creation and validation steps due to low genome sequence quality is possibly the main reason for this result. The cgMLST scheme was compared with previously published whole genome single nucleotide polymorphism analysis for the characterization of the population structure of the epidemic clone ST235 and results were highly similar. In order to evaluate the typing resolution of the proposed scheme, collections of isolates belonging to two important STs associated with cystic fibrosis, ST146 and ST274, were typed using this scheme, and ST235 isolates associated with an outbreak were evaluated. Besides confirming the relatedness of all the isolates, earlier determined by MLST, the higher resolution of cgMLST denotes that it may be suitable for surveillance programs, overcoming possible shortcomings of classical MLST. The proposed scheme is publicly available at: https://github.com/BioinformaticsHIAEMolecularMicrobiology/cgMLST-Pseudomonas-aeruginosa.
Collapse
Affiliation(s)
- Romário Oliveira de Sales
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Letícia Busato Migliorini
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Renato Puga
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| | - Bela Kocsis
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Patricia Severino
- Hospital Israelita Albert Einstein, Albert Einstein Research and Education Institute, São Paulo, Brazil
| |
Collapse
|
7
|
Snyman Y, Whitelaw AC, Reuter S, Dramowski A, Maloba MRB, Newton-Foot M. Clonal expansion of colistin-resistant Acinetobacter baumannii isolates in Cape Town, South Africa. Int J Infect Dis 2019; 91:94-100. [PMID: 31765820 DOI: 10.1016/j.ijid.2019.11.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVES To describe colistin-resistant Acinetobacter baumannii isolates in Cape Town, South Africa. METHODS A. baumannii isolates identified on Vitek 2 Advanced Expert System were collected from Tygerberg Hospital referral laboratory between 2016 and 2017. Colistin resistance was confirmed using broth microdilution and SensiTest. mcr-1-5 were detected using PCR and strain typing was performed by rep-PCR. Whole genome sequencing (WGS) was performed on a subset of isolates to identify chromosomal colistin resistance mechanisms and strain diversity using multilocus sequence typing (MLST) and pairwise single nucleotide polymorphism analyses. RESULTS Twenty-six colistin-resistant and six colistin-susceptible A. baumannii were collected separately based on Vitek susceptibility; 20/26 (77%) were confirmed colistin-resistant by broth microdilution. Four colistin-resistant isolates were isolated in 2016 and 16 in 2017, from five healthcare facilities. Thirteen colistin-resistant isolates and eight colistin-susceptible isolates were identical by rep-PCR and MLST (ST1), all from patients admitted to a tertiary hospital during 2017. The remaining colistin-resistant isolates were unrelated. CONCLUSIONS An increase in colistin-resistant A. baumannii isolates from a tertiary hospital in 2017 appears to be clonal expansion of an emerging colistin-resistant strain. This strain was not detected in 2016 or from other hospitals. Identical colistin-susceptible isolates were also isolated, suggesting relatively recent acquisition of colistin resistance.
Collapse
Affiliation(s)
- Yolandi Snyman
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Cape Town, South Africa.
| | - Andrew Christopher Whitelaw
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Cape Town, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Stellenbosch University, Cape Town, South Africa
| | - Motlatji Reratilwe Bonnie Maloba
- Department of Medical Microbiology, University of the Free State, Bloemfontein, South Africa; National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Mae Newton-Foot
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Cape Town, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| |
Collapse
|
8
|
Rafei R, Osman M, Dabboussi F, Hamze M. Update on the epidemiological typing methods for Acinetobacter baumannii. Future Microbiol 2019; 14:1065-1080. [DOI: 10.2217/fmb-2019-0134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The outstanding ability of Acinetobacter baumannii to cause outbreaks and acquire multidrug resistance motivated the development of a plethora of typing techniques, which can help infection preventionists and hospital epidemiologists to more efficiently implement intervention controls. Nowadays, the world is witnessing a gradual transition from traditional typing methodology to whole genome sequencing-based approaches. Such approaches are opening new prospects and applications never achieved by existing typing methods. Herein, we provide the reader with an updated review on A. baumannii typing methods recapping the added value of well-established techniques previously applied for A. baumannii and detailing new ones (as clustered regularly interspaced short palindromic repeats-based typing) with a special focus on whole genome sequencing.
Collapse
Affiliation(s)
- Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| |
Collapse
|
9
|
Epidemiological investigation of an Acinetobacter baumannii outbreak using core genome multilocus sequence typing. J Glob Antimicrob Resist 2018; 17:245-249. [PMID: 30553929 DOI: 10.1016/j.jgar.2018.11.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES Carbapenem-resistant Acinetobacter baumannii (CRAB) is a serious nosocomial pathogen that causes a variety of serious, often life-threatening, infections and outbreaks. This study aimed to investigate the molecular epidemiology of clinical CRAB isolates from an outbreak that occurred in the intensive care unit (ICU) of an Italian hospital. METHODS From December 2016 to April 2017, 13 CRAB isolates were collected from seven patients treated in the ICU at 'L. Spallanzani' Hospital (Rome, Italy). Typing was performed by repetitive extragenic palindromic PCR (rep-PCR) using a DiversiLab® system. Whole-genome sequencing (WGS) data were used for in silico analysis of traditional multilocus sequence typing (MLST) results, to identify resistance genes and for core genome MLST (cgMLST) analysis. Epidemiological data were obtained from hospital records. RESULTS All isolates showed a carbapenem-resistant profile and carried the blaOXA-23 carbapenemase gene. Typing performed by rep-PCR and MLST showed that the isolates clustered into one group, whilst the cgMLST approach, which uses 2390 gene targets to characterise the gene-by-gene allelic profile, highlighted the presence of two cluster types. These results allowed us to identify two patients who were likely to be the source of two separate transmission chains. CONCLUSION These results show that WGS by cgMLST is a valuable tool, better suited for prompt epidemiological investigations than traditional typing methods because of its higher discriminatory ability in determining clonal relatedness.
Collapse
|
10
|
Nosocomial Outbreak of Extensively Drug-Resistant Acinetobacter baumannii Isolates Containing blaOXA-237 Carried on a Plasmid. Antimicrob Agents Chemother 2017; 61:AAC.00797-17. [PMID: 28893775 DOI: 10.1128/aac.00797-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/22/2017] [Indexed: 11/20/2022] Open
Abstract
Carbapenem antibiotics are among the mainstays for treating infections caused by Acinetobacter baumannii, especially in the Northwest United States, where carbapenem-resistant A. baumannii remains relatively rare. However, between June 2012 and October 2014, an outbreak of carbapenem-resistant A. baumannii occurred in 16 patients from five health care facilities in the state of Oregon. All isolates were defined as extensively drug resistant. Multilocus sequence typing revealed that the isolates belonged to sequence type 2 (international clone 2 [IC2]) and were >95% similar as determined by repetitive-sequence-based PCR analysis. Multiplex PCR revealed the presence of a blaOXA carbapenemase gene, later identified as blaOXA-237 Whole-genome sequencing of all isolates revealed a well-supported separate branch within a global A. baumannii phylogeny. Pacific Biosciences (PacBio) SMRT sequencing was also performed on one isolate to gain insight into the genetic location of the carbapenem resistance gene. We discovered that blaOXA-237, flanked on either side by ISAba1 elements in opposite orientations, was carried on a 15,198-bp plasmid designated pORAB01-3 and was present in all 16 isolates. The plasmid also contained genes encoding a TonB-dependent receptor, septicolysin, a type IV secretory pathway (VirD4 component, TraG/TraD family) ATPase, an integrase, a RepB family plasmid DNA replication initiator protein, an alpha/beta hydrolase, and a BrnT/BrnA type II toxin-antitoxin system. This is the first reported outbreak in the northwestern United States associated with this carbapenemase. Particularly worrisome is that blaOXA-237 was carried on a plasmid and found in the most prominent worldwide clonal group IC2, potentially giving pORAB01-3 great capacity for future widespread dissemination.
Collapse
|
11
|
Wilharm G, Skiebe E, Higgins PG, Poppel MT, Blaschke U, Leser S, Heider C, Heindorf M, Brauner P, Jäckel U, Böhland K, Cuny C, Łopińska A, Kaminski P, Kasprzak M, Bochenski M, Ciebiera O, Tobółka M, Żołnierowicz KM, Siekiera J, Seifert H, Gagné S, Salcedo SP, Kaatz M, Layer F, Bender JK, Fuchs S, Semmler T, Pfeifer Y, Jerzak L. Relatedness of wildlife and livestock avian isolates of the nosocomial pathogenAcinetobacter baumanniito lineages spread in hospitals worldwide. Environ Microbiol 2017; 19:4349-4364. [DOI: 10.1111/1462-2920.13931] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 09/14/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Gottfried Wilharm
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Evelyn Skiebe
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene; University of Cologne; Cologne D-50935 Germany
- Partner site Bonn-Cologne; German Centre for Infection Research (DZIF); Germany
| | - Marie T. Poppel
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Ulrike Blaschke
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Sarah Leser
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Christine Heider
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Magdalena Heindorf
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Paul Brauner
- Federal Institute for Occupational Safety and Health (BAuA), Nöldnerstr. 40-42; Berlin D-10317 Germany
| | - Udo Jäckel
- Federal Institute for Occupational Safety and Health (BAuA), Nöldnerstr. 40-42; Berlin D-10317 Germany
| | | | - Christiane Cuny
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Andżelina Łopińska
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
| | - Piotr Kaminski
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
- Nicolaus Copernicus University in Toruń, Collegium Medicum in Bydgoszcz, Faculty of Medicine; Department of Medical Biology, Department of Ecology and Environmental Protection; M. Skłodowska-Curie St. 9, PL 85-094 Bydgoszcz Poland
| | - Mariusz Kasprzak
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
| | - Marcin Bochenski
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
| | - Olaf Ciebiera
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
| | - Marcin Tobółka
- Institute of Zoology; Poznań University of Life Sciences, Wojska Polskiego 71C; 60-625 Poznań Poland
| | - Katarzyna M. Żołnierowicz
- Institute of Zoology; Poznań University of Life Sciences, Wojska Polskiego 71C; 60-625 Poznań Poland
| | | | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene; University of Cologne; Cologne D-50935 Germany
- Partner site Bonn-Cologne; German Centre for Infection Research (DZIF); Germany
| | - Stéphanie Gagné
- Laboratory of Molecular Microbiology and Structural Biochemistry; University of Lyon, CNRS UMR 5086; Lyon F-69367 France
| | - Suzana P. Salcedo
- Laboratory of Molecular Microbiology and Structural Biochemistry; University of Lyon, CNRS UMR 5086; Lyon F-69367 France
| | - Michael Kaatz
- Vogelschutzwarte Storchenhof Loburg e.V, Chausseestr. 18; Loburg D-39279 Germany
| | - Franziska Layer
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Jennifer K. Bender
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Stephan Fuchs
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | | | - Yvonne Pfeifer
- Wernigerode Branch; Robert Koch Institute, Burgstr. 37; Wernigerode D-38855 Germany
| | - Leszek Jerzak
- Faculty of Biological Sciences; University of Zielona Góra, Prof. Z. Szafrana Street 1; 65-561 Zielona Góra Poland
| |
Collapse
|
12
|
Newton-Foot M, Snyman Y, Maloba MRB, Whitelaw AC. Plasmid-mediated mcr-1 colistin resistance in Escherichia coli and Klebsiella spp. clinical isolates from the Western Cape region of South Africa. Antimicrob Resist Infect Control 2017; 6:78. [PMID: 28785405 PMCID: PMC5543748 DOI: 10.1186/s13756-017-0234-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/25/2017] [Indexed: 12/02/2022] Open
Abstract
Background Colistin is a last resort antibiotic for the treatment of carbapenem-resistant Gram negative infections. Until recently, mechanisms of colistin resistance were limited to chromosomal mutations which confer a high fitness cost and cannot be transferred between organisms. However, a novel plasmid-mediated colistin resistance mechanism, encoded by the mcr-1 gene, has been identified, and has since been detected worldwide. The mcr-1 colistin resistance mechanism is a major threat due to its lack of fitness cost and ability to be transferred between strains and species. Surveillance of colistin resistance mechanisms is critical to monitor the development and spread of resistance.This study aimed to determine the prevalence of the plasmid-mediated colistin resistance gene, mcr-1, in colistin-resistant E. coli and Klebsiella spp. isolates in the Western Cape of South Africa; and whether colistin resistance is spread through clonal expansion or by acquisition of resistance by diverse strains. Methods Colistin resistant E. coli and Klebsiella spp. isolates were collected from the NHLS microbiology laboratory at Tygerberg Hospital. Species identification and antibiotic susceptibility testing was done using the API® 20 E system and the Vitek® 2 Advanced Expert System™. PCR was used to detect the plasmid-mediated mcr-1 colistin resistance gene and REP-PCR was used for strain typing of the isolates. Results Nineteen colistin resistant isolates, including 12 E. coli, six K. pneumoniae and one K. oxytoca isolate, were detected over 7 months from eight different hospitals in the Western Cape region. The mcr-1 gene was detected in 83% of isolates which were shown to be predominantly unrelated strains. Conclusions The plasmid-mediated mcr-1 colistin resistance gene is responsible for the majority of colistin resistance in clinical isolates of E. coli and Klebsiella spp. from the Western Cape of South Africa. Colistin resistance is not clonally disseminated; the mcr-1 gene has been acquired by several unrelated strains of E. coli and K. pneumoniae. Acquisition of mcr-1 by cephalosporin- and carbapenem-resistant Gram negative bacteria may result in untreatable infections and increased mortality. Measures need to be implemented to control the use of colistin in health care facilities and in agriculture to retain its antimicrobial efficacy.
Collapse
Affiliation(s)
- Mae Newton-Foot
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Cape Town, South Africa.,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Yolandi Snyman
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Cape Town, South Africa
| | - Motlatji Reratilwe Bonnie Maloba
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Cape Town, South Africa.,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Andrew Christopher Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Cape Town, South Africa.,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| |
Collapse
|
13
|
Carbapenem-Resistant Klebsiella pneumoniae: Results of a Laboratory Surveillance Program in an Italian General Hospital (August 2014-January 2015) : Surveillance of Carbapenem-resistant Klebsiella pneumoniae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [PMID: 26810235 DOI: 10.1007/5584_2015_5018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
In this study we report the analysis of 131 Klebsiella pneumoniae (K. pneumoniae) clinical isolates from patients hospitalized in various wards, of Perugia General Hospital, from August 2014 to January 2015. Forty two isolates (32.1 %), were resistant to at least one carbapenem antibiotic and, among these isolates, 14 (33.3 %) exhibited resistance to colistin. All isolates were carbapenemases producers and 41 (97.6 %) harboured the bla KPC gene. Carbapenem-resistant K. pneumoniae isolates (CRKPs) were, also, typed for the genotypic diversity and the results revealed the circulation of two major clusters.This surveillance study evidences the spread of CRKP isolates in Perugia General Hospital and confirms that carbapenem-resistant K. pneumoniae isolates have reached epidemic dissemination in Italy. In addition the percentage of resistance to colistin resulted to be less than that observed in other hospital laboratories across Italy. In conclusion the circulation of these isolates should be monitored and appropriate policy of surveillance must be used, in a target manner, in order to reduce the spread of carbapenem-resistant isolates.
Collapse
|
14
|
Higgins PG, Prior K, Harmsen D, Seifert H. Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii. PLoS One 2017; 12:e0179228. [PMID: 28594944 PMCID: PMC5464626 DOI: 10.1371/journal.pone.0179228] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/25/2017] [Indexed: 01/05/2023] Open
Abstract
We have employed whole genome sequencing to define and evaluate a core genome multilocus sequence typing (cgMLST) scheme for Acinetobacter baumannii. To define a core genome we downloaded a total of 1,573 putative A. baumannii genomes from NCBI as well as representative isolates belonging to the eight previously described international A. baumannii clonal lineages. The core genome was then employed against a total of fifty-three carbapenem-resistant A. baumannii isolates that were previously typed by PFGE and linked to hospital outbreaks in eight German cities. We defined a core genome of 2,390 genes of which an average 98.4% were called successfully from 1,339 A. baumannii genomes, while Acinetobacter nosocomialis, Acinetobacter pittii, and Acinetobacter calcoaceticus resulted in 71.2%, 33.3%, and 23.2% good targets, respectively. When tested against the previously identified outbreak strains, we found good correlation between PFGE and cgMLST clustering, with 0–8 allelic differences within a pulsotype, and 40–2,166 differences between pulsotypes. The highest number of allelic differences was between the isolates representing the international clones. This typing scheme was highly discriminatory and identified separate A. baumannii outbreaks. Moreover, because a standardised cgMLST nomenclature is used, the system will allow inter-laboratory exchange of data.
Collapse
Affiliation(s)
- Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
- * E-mail:
| | - Karola Prior
- Department for Periodontology and Restorative Dentistry, University Hospital Muenster, Muenster, Germany
| | - Dag Harmsen
- Department for Periodontology and Restorative Dentistry, University Hospital Muenster, Muenster, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| |
Collapse
|
15
|
Viau RA, Kiedrowski LM, Kreiswirth BN, Adams M, Perez F, Marchaim D, Guerrero DM, Kaye KS, Logan LK, Villegas MV, Bonomo RA. A Comparison of Molecular Typing Methods Applied to Enterobacter cloacae complex: hsp60 Sequencing, Rep-PCR, and MLST. Pathog Immun 2017; 2:23-33. [PMID: 28428984 PMCID: PMC5394936 DOI: 10.20411/pai.v2i1.99] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Molecular typing using repetitive sequenced-based PCR (rep-PCR) and hsp60 sequencing were applied to a collection of diverse Enterobacter cloacae complex isolates. To determine the most practical method for reference laboratories, we analyzed 71 E. cloacae complex isolates from sporadic and outbreak occurrences originating from 4 geographic areas. While rep-PCR was more discriminating, hsp60 sequencing provided a broader and a more objective geographical tracking method similar to multilocus sequence typing (MLST). In addition, we suggest that MLST may have higher discriminative power compared to hsp60 sequencing, although rep-PCR remains the most discriminative method for local outbreak investigations. In addition, rep-PCR can be an effective and inexpensive method for local outbreak investigation.
Collapse
Affiliation(s)
- Roberto A Viau
- Medical and Research Services Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | | | - Barry N Kreiswirth
- Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, NJ
| | | | - Federico Perez
- Medical and Research Services Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - Dror Marchaim
- Department of Medicine, Infection Control and Prevention Unit of Infectious Diseases, Assaf Harofeh Medical Center
| | | | - Keith S Kaye
- Wayne State University and Detroit Medical Center, Detroit, MI
| | - Latania K Logan
- Medical and Research Services Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH.,Rush University Medical Center, Chicago, IL
| | | | - Robert A Bonomo
- Medical and Research Services Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH.,Departments of Medicine, Microbiology and Cellular Biology, and Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH
| |
Collapse
|
16
|
Clonal Spread of Acinetobacter baumannii Sequence Type 25 Carrying blaOXA-23 in Companion Animals in France. Antimicrob Agents Chemother 2016; 61:AAC.01881-16. [PMID: 27799214 DOI: 10.1128/aac.01881-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
17
|
De Vos D, Pirnay JP, Bilocq F, Jennes S, Verbeken G, Rose T, Keersebilck E, Bosmans P, Pieters T, Hing M, Heuninckx W, De Pauw F, Soentjens P, Merabishvili M, Deschaght P, Vaneechoutte M, Bogaerts P, Glupczynski Y, Pot B, van der Reijden TJ, Dijkshoorn L. Molecular Epidemiology and Clinical Impact of Acinetobacter calcoaceticus-baumannii Complex in a Belgian Burn Wound Center. PLoS One 2016; 11:e0156237. [PMID: 27223476 PMCID: PMC4880317 DOI: 10.1371/journal.pone.0156237] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 05/11/2016] [Indexed: 12/21/2022] Open
Abstract
Multidrug resistant Acinetobacter baumannii and its closely related species A. pittii and A. nosocomialis, all members of the Acinetobacter calcoaceticus-baumannii (Acb) complex, are a major cause of hospital acquired infection. In the burn wound center of the Queen Astrid military hospital in Brussels, 48 patients were colonized or infected with Acb complex over a 52-month period. We report the molecular epidemiology of these organisms, their clinical impact and infection control measures taken. A representative set of 157 Acb complex isolates was analyzed using repetitive sequence-based PCR (rep-PCR) (DiversiLab) and a multiplex PCR targeting OXA-51-like and OXA-23-like genes. We identified 31 rep-PCR genotypes (strains). Representatives of each rep-type were identified to species by rpoB sequence analysis: 13 types to A. baumannii, 10 to A. pittii, and 3 to A. nosocomialis. It was assumed that isolates that belonged to the same rep-type also belonged to the same species. Thus, 83.4% of all isolates were identified to A. baumannii, 9.6% to A. pittii and 4.5% to A. nosocomialis. We observed 12 extensively drug resistant Acb strains (10 A. baumannii and 2 A. nosocomialis), all carbapenem-non-susceptible/colistin-susceptible and imported into the burn wound center through patients injured in North Africa. The two most prevalent rep-types 12 and 13 harbored an OXA-23-like gene. Multilocus sequence typing allocated them to clonal complex 1 corresponding to EU (international) clone I. Both strains caused consecutive outbreaks, interspersed with periods of apparent eradication. Patients infected with carbapenem resistant A. baumannii were successfully treated with colistin/rifampicin. Extensive infection control measures were required to eradicate the organisms. Acinetobacter infection and colonization was not associated with increased attributable mortality.
Collapse
Affiliation(s)
- Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
- * E-mail:
| | - Florence Bilocq
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Serge Jennes
- Burn Wound Center, Queen Astrid Military Hospital, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Thomas Rose
- Burn Wound Center, Queen Astrid Military Hospital, Brussels, Belgium
| | | | - Petra Bosmans
- Hospital Hygiene and Infection Control Team, Queen Astrid Military Hospital, Brussels, Belgium
| | - Thierry Pieters
- Hospital Hygiene and Infection Control Team, Queen Astrid Military Hospital, Brussels, Belgium
| | - Mony Hing
- Clinical Laboratory, Queen Astrid Military Hospital, Brussels, Belgium
| | - Walter Heuninckx
- Clinical Laboratory, Queen Astrid Military Hospital, Brussels, Belgium
| | - Frank De Pauw
- Medical Communication and Information Systems, ACOS WB/Health Division, Queen Astrid Military Hospital, Brussels, Belgium
| | - Patrick Soentjens
- Burn Wound Center, Queen Astrid Military Hospital, Brussels, Belgium
| | - Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
- Laboratory Bacteriology Research, University of Ghent, Ghent, Belgium
| | - Pieter Deschaght
- Laboratory Bacteriology Research, University of Ghent, Ghent, Belgium
| | | | - Pierre Bogaerts
- Laboratoire de Bactériologie, CHU Mont-Godinne, Université Catholique de Louvain, Yvoir, Belgium
| | - Youri Glupczynski
- Laboratoire de Bactériologie, CHU Mont-Godinne, Université Catholique de Louvain, Yvoir, Belgium
| | - Bruno Pot
- Applied Maths, Sint-Martens-Latem, Belgium
| | - Tanny J. van der Reijden
- Department of Infectious Diseases C5-P, Leiden University Medical Center, Leiden, The Netherlands
| | - Lenie Dijkshoorn
- Department of Infectious Diseases C5-P, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
18
|
Granzer H, Hagen RM, Warnke P, Bock W, Baumann T, Schwarz NG, Podbielski A, Frickmann H, Koeller T. Molecular Epidemiology of Carbapenem-Resistant Acinetobacter Baumannii Complex Isolates from Patients that were Injured During the Eastern Ukrainian Conflict. Eur J Microbiol Immunol (Bp) 2016; 6:109-17. [PMID: 27429793 PMCID: PMC4936333 DOI: 10.1556/1886.2016.00014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 12/30/2022] Open
Abstract
This study addressed carbapenem-resistant Acinetobacter baumannii complex (ABC) isolates from patients that were injured during the military conflict in the Eastern Ukraine and treated at German Armed Forces Hospitals in 2014 and 2015. Clonal diversity of the strains and potential ways of transmission were analyzed. Patients with one or several isolation events of carbapenem-resistant ABC were included. Isolates were characterized by VITEK II-based identification and resistance testing, molecular screening for frequent carbapenemase genes, and DiversiLab rep-PCR-based typing. Available clinical information of the patients was assessed. From 21 young male Ukrainian patients with battle injuries, 32 carbapenem- and fluoroquinolone-resistant ABC strains were isolated. Four major clonal clusters were detected. From four patients (19%), ABC isolates from more than one clonal cluster were isolated. The composition of the clusters suggested transmission events prior to the admission to the German hospitals. The infection and colonization pressure in the conflict regions of the Eastern Ukraine with ABC of low clonal diversity is considerable. Respective infection risks have to be considered in case of battle-related injuries in these regions. The low number of local clones makes any molecular exclusion of transmission events difficult.
Collapse
Affiliation(s)
- Heike Granzer
- Laboratory Department I, Central Institute of the German Armed Forces in Koblenz , Germany
| | - Ralf Matthias Hagen
- North Atlantic Treaty Organization Center of Excellence in Military Medicine (NATO MilMedCOE) , Munich, Germany
| | - Philipp Warnke
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock , Germany
| | - Wolfgang Bock
- Laboratory Department I, Central Institute of the German Armed Forces in Munich , Germany
| | - Tobias Baumann
- Laboratory Department I, Central Institute of the German Armed Forces in Kiel (branch office in Berlin) , Germany
| | - Norbert Georg Schwarz
- Infectious Disease Epidemiology Group, Bernhard Nocht Institute of Tropical Medicine Hamburg , Germany
| | - Andreas Podbielski
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock , Germany
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Germany; Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Germany
| | - Thomas Koeller
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock , Germany
| |
Collapse
|
19
|
Kashiwaya K, Saga T, Ishii Y, Sakata R, Iwata M, Yoshizawa S, Chang B, Ohnishi M, Tateda K. Worldwide Lineages of Clinical Pneumococci in a Japanese Teaching Hospital Identified by DiversiLab System. J Infect Chemother 2016; 22:407-13. [PMID: 27107736 DOI: 10.1016/j.jiac.2016.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/11/2016] [Accepted: 03/16/2016] [Indexed: 11/19/2022]
Abstract
Pneumococcal Molecular Epidemiology Network (PMEN) clones are representatives of worldwide-spreading pathogens. DiversiLab system, a repetitive PCR system, has been proposed as a less labor-and time-intensive genotyping platform alternative to conventional methods. However, the utility and analysis parameters of DiversiLab for identifying worldwide lineages was not established. To evaluate and optimize the performance of DiversiLab for identifying worldwide pneumococcal lineages, we examined 245 consecutive isolates of clinical Streptococcus pneumoniae from all age-group patients at a teaching hospital in Japan. The capsular swelling reaction of all isolates yielded 24 different serotypes. Intensive visual observation (VO) of DiversiLab band pattern difference divided all isolates into 73 clusters. Multilocus sequence typing (MLST) of representative 73 isolates from each VO cluster yielded 51 different STs. Among them, PMEN-related lineages accounted for 63% (46/73). Although the serotype of PMEN-related isolates was identical to that of the original PMEN clone in 70% (32/46), CC156-related PMEN lineages, namely Greece(6B)-22 and Colombia(23F)-26, harbored various capsular types discordant to the original PMEN clones. Regarding automated analysis, genotyping by extended Jaccard (XJ) with a 75% similarity index cutoff (SIC) showed the highest correlation with serotyping (adjusted Rand's coefficient, 0.528). Elevating the SIC for XJ to 85% increased the discriminatory power sufficient for distinguishing two major PMEN-related isolates of Taiwan(19F)-14 and Netherlands(3)-31. These results demonstrated a potential utility of DiversiLab for identifying worldwide lineage of pneumococcus. An optimized parameters of automated analysis should be useful especially for comparison for reference strains by "identification" function of DiversiLab.
Collapse
Affiliation(s)
- Kiyoshi Kashiwaya
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Department of Clinical Laboratory, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Tomoo Saga
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Central Laboratory Division, Akita University Hospital, Akita, Japan.
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Ryuji Sakata
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Morihiro Iwata
- Clinical Laboratory Department, Toho University Omori Medical Center, Tokyo, Japan
| | - Sadako Yoshizawa
- Division of Infection Control, Toho University Omori Medical Center, Tokyo, Japan
| | - Bin Chang
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Clinical Laboratory Department, Toho University Omori Medical Center, Tokyo, Japan; Division of Infection Control, Toho University Omori Medical Center, Tokyo, Japan
| |
Collapse
|
20
|
Tomaschek F, Higgins PG, Stefanik D, Wisplinghoff H, Seifert H. Head-to-Head Comparison of Two Multi-Locus Sequence Typing (MLST) Schemes for Characterization of Acinetobacter baumannii Outbreak and Sporadic Isolates. PLoS One 2016; 11:e0153014. [PMID: 27071077 PMCID: PMC4829225 DOI: 10.1371/journal.pone.0153014] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
To compare the two Acinetobacter baumannii multi-locus sequence typing (MLST) schemes and to assess their suitability to aid in outbreak analysis we investigated the molecular epidemiology of 99 Acinetobacter baumannii isolates representing outbreak-related and sporadic isolates from 24 hospitals in four different countries (Germany, Poland, Sweden, and Turkey). Pulsed-field gel electrophoresis (PFGE) was used as the reference method to determine the epidemiologic relatedness of isolates and compared to MLST using both the Oxford and Pasteur scheme. Rep-PCR was used to define international clonal lineages (IC). We identified 26 unique outbreak strains and 21 sporadic strains. The majority of outbreaks were associated with carbapenem-resistant A. baumannii harbouring oxacillinase OXA-23-like and corresponding to IC 2. Sequence types (STs) obtained from the Oxford scheme correlate well with PFGE patterns, while the STs of the Pasteur scheme are more in accordance with rep-PCR grouping, but neither one is mirroring completely the results of the comparator. On two occasions the Oxford scheme identified two different STs within a single outbreak where PFGE patterns had only one band difference. The CCs of both MLST schemes were able to define clonal clusters that were concordant with the ICs determined by rep-PCR. IC4 corresponds to the previously described CC15 Pasteur (= CC103 Oxford). It can be concluded that both MLST schemes are valuable tools for population-based studies. In addition, the higher discriminatory power of the Oxford scheme that compares with the resolution obtained with PFGE can often aid in outbreak analysis.
Collapse
Affiliation(s)
- Franziska Tomaschek
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Cologne-Bonn, Cologne, Germany
| | - Danuta Stefanik
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Hilmar Wisplinghoff
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Cologne-Bonn, Cologne, Germany
- * E-mail:
| |
Collapse
|
21
|
Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks. J Clin Microbiol 2015; 54:593-612. [PMID: 26699703 DOI: 10.1128/jcm.01818-15] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/17/2015] [Indexed: 12/21/2022] Open
Abstract
Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The band-based techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts.
Collapse
|
22
|
Wu M, Li H, Jiang Y, Song C, Guo H, Wu S, Liu C, Li J, Zeng H, Zhai X, Zhang W, Fan E, Liu Q. Simultaneous quantification of Escherichia coli O157:H7 and Shigella boydii using a visual-antibody-macroarray. Analyst 2015; 140:6595-601. [PMID: 26300105 DOI: 10.1039/c5an01035g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Being high throughput, rapid, automated, economical, convenient to operate and highly sensitive, protein arrays have been widely used in the analysis of tumor markers and veterinary drug residues. Pathogenic microbes also can be detected qualitatively by DNA array or protein array; however, their high throughput detection and quantification remains a big obstacle. To evaluate the potentiality of protein arrays for multiple quantitative detection of microorganisms with naked eye examination without the help of any equipment, here we developed a visual-antibody-macroarray (VAMA) aiming at rapid and simultaneous quantification of Escherichia coli O157:H7 and Shigella boydii. The results show that this VAMA is highly specific and is able to distinguish mixed Escherichia coli O157:H7 and Shigella boydii synchronously. The detection limits are equivalent to 3.4 × 10(5) CFU mL(-1) and 3.2 × 10(5) CFU mL(-1), respectively, which conform to the results of plate counting and ELISA. Importantly, the examination can be solely performed with the naked eye. Therefore, we provide an easy, reliable and rapid method for quantitative analysis of microorganisms.
Collapse
Affiliation(s)
- Man Wu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Bedenić B, Beader N, Godič-Torkar K, Vranić-Ladavac M, Luxner J, Veir Z, Grisold AJ, Zarfel G. Nursing Home as a Reservoir of Carbapenem-ResistantAcinetobacter baumannii. Microb Drug Resist 2015; 21:270-8. [DOI: 10.1089/mdr.2014.0157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Branka Bedenić
- Department of Microbiology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical and Molecular Microbiology, Clinical Hospital Center Zagreb, Zagreb, Croatia
| | - Nataša Beader
- Department of Microbiology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical and Molecular Microbiology, Clinical Hospital Center Zagreb, Zagreb, Croatia
| | - Karmen Godič-Torkar
- Department for Sanitary Engineering, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Mirna Vranić-Ladavac
- Department of Microbiology, Public Health Institute of Istria County, Pula, Croatia
| | - Josefa Luxner
- Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Zoran Veir
- Department of Surgery, Clinical Hospital Center Zagreb, Zagreb, Croatia
| | - Andrea J. Grisold
- Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Gernot Zarfel
- Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| |
Collapse
|
24
|
Anderson KM, Abbott J, Zhao S, Liu E, Himathongkham S. Molecular Subtyping of Shiga Toxin-Producing Escherichia coli Using a Commercial Repetitive Sequence-Based PCR Assay. J Food Prot 2015; 78:902-11. [PMID: 25951383 DOI: 10.4315/0362-028x.jfp-14-430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
PCR-based typing methods, such as repetitive sequence-based PCR (rep-PCR), may facilitate the identification of Shiga toxin-producing Escherichia coli (STEC) by serving as screening methods to reduce the number of isolates to be processed for further confirmation. In this study, we used a commercial rep-PCR typing system to generate DNA fingerprint profiles for STEC O157 (n = 60) and non-O157 (n = 91) isolates from human, food, and animal samples and then compared the results with those obtained from pulsed-field gel electrophoresis (PFGE). Fifteen serogroups were analyzed using the Kullback Leibler or extended Jaccard statistical method, and the unweighted pair group method of averages algorithm was used to create dendrograms. Among the 151 STEC isolates tested, all were typeable by rep-PCR. Among the non-O157 isolates, rep-PCR clustered 79 (88.8%) of 89 isolates according to serogroup status, with peak differences ranging from 1 (96.4% similarity) to 12 (58.7% similarity). The genetic relatedness of the non-O157 serogroups mirrored the branching of distinct clonal groups elucidated by other investigators. Although the discriminatory power of rep-PCR (Simpson's index of diversity [SID] = 0.954) for the O157 isolates was less than that of PFGE (SID = 0.993), rep-PCR was able to identify 29 pattern types, suggesting that this method can be used for strain typing, although not to the same level as PFGE. Similar results were obtained from analysis of the non-O157 isolates. With rep-PCR, we assigned non-O157 isolates to 46 pattern types with a SID of 0.977. By PFGE, non-O157 STEC strains were divided into 77 pattern types with a SID of 0.996. Together, these results indicate the ability of the rep-PCR typing system to distinguish between and within O157 and non-O157 STEC groups. Rapid PCR-based typing methods could be invaluable tools for use in outbreak investigations by excluding unrelated STEC isolates within 24 h.
Collapse
Affiliation(s)
- Kimberly M Anderson
- U.S. Food and Drug Administration, Office of Regulatory Affairs, San Francisco District Laboratory, Alameda, California 94502, USA.
| | - Jason Abbott
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland 20708, USA
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland 20708, USA
| | - Eileen Liu
- U.S. Food and Drug Administration, Office of Regulatory Affairs, San Francisco District Laboratory, Alameda, California 94502, USA
| | - Sunee Himathongkham
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Office of Regulatory Science, Rockville, Maryland 20857, USA
| |
Collapse
|
25
|
Townsend J, Park AN, Gander R, Orr K, Arocha D, Zhang S, Greenberg DE. Acinetobacter infections and outcomes at an academic medical center: a disease of long-term care. Open Forum Infect Dis 2015; 2:ofv023. [PMID: 26034772 PMCID: PMC4438902 DOI: 10.1093/ofid/ofv023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/12/2015] [Indexed: 11/14/2022] Open
Abstract
Background. Our study aims to describe the epidemiology, microbial resistance patterns, and clinical outcomes of Acinetobacter infections at an academic university hospital. This retrospective study analyzed all inpatient clinical isolates of Acinetobacter collected at an academic medical center over 4 years. The data were obtained from an Academic tertiary referral center between January 2008 and December 2011. All consecutive inpatients during the study period who had a clinical culture positive for Acinetobacter were included in the study. Patients without medical records available for review or less than 18 years of age were excluded. Methods. Records were reviewed to determine source of isolation, risk factors for acquisition, drug resistance patterns, and clinical outcomes. Repetitive sequence-based polymerase chain reaction of selected banked isolates was used to determine patterns of clonal spread in and among institutions during periods of higher infection rates. Results. Four hundred eighty-seven clinical isolates of Acinetobacter were found in 212 patients (in 252 admissions). Patients with Acinetobacter infections were frequently admitted from healthcare facilities (HCFs) (59%). One hundred eighty-three of 248 (76%) initial isolates tested were resistant to meropenem. One hundred ninety-eight of 249 (79.5%) initial isolates were multidrug resistant (MDR). Factors associated with mortality included bacteremia (odds ratio [OR] = 1.93, P = .024), concomitant steroid use (OR = 2.87, P < .001), admission from a HCF (OR = 6.34, P = .004), and chronic obstructive pulmonary disease (OR = 3.17, P < .001). Conclusions. Acinetobacter isolates at our institution are frequently MDR and are more common among those who reside in HCFs. Our findings underline the need for new strategies to prevent and treat this pathogen, including stewardship efforts in long-term care settings.
Collapse
Affiliation(s)
| | | | | | - Kathleen Orr
- Microbiology Laboratory , Parkland Health and Hospital System
| | - Doramarie Arocha
- Division of Infection Prevention , University Hospital Administration, St. Paul University Hospital
| | - Song Zhang
- Division of Biostatistics, Department of Clinical Sciences , University of Texas Southwestern , Dallas, Texas
| | | |
Collapse
|
26
|
Rafei R, Dabboussi F, Hamze M, Eveillard M, Lemarié C, Gaultier MP, Mallat H, Moghnieh R, Husni-Samaha R, Joly-Guillou ML, Kempf M. Molecular analysis of Acinetobacter baumannii strains isolated in Lebanon using four different typing methods. PLoS One 2014; 9:e115969. [PMID: 25541711 PMCID: PMC4277430 DOI: 10.1371/journal.pone.0115969] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 12/03/2014] [Indexed: 12/13/2022] Open
Abstract
This study analyzed 42 Acinetobacter baumannii strains collected between 2009–2012 from different hospitals in Beyrouth and North Lebanon to better understand the epidemiology and carbapenem resistance mechanisms in our collection and to compare the robustness of pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), repetitive sequence-based PCR (rep-PCR) and blaOXA-51 sequence-based typing (SBT). Among 31 carbapenem resistant strains, we have detected three carbapenem resistance genes: 28 carried the blaOXA-23 gene, 1 the blaOXA-24 gene and 2 strains the blaOXA-58 gene. This is the first detection of blaOXA-23 and blaOXA-24 in Lebanon. PFGE identified 11 types and was the most discriminating technique followed by rep-PCR (9 types), blaOXA-51 SBT (8 types) and MLST (7 types). The PFGE type A'/ST2 was the dominant genotype in our collection present in Beyrouth and North Lebanon. The clustering agreement between all techniques was measured by adjust Wallace coefficient. An overall agreement has been demonstrated. High values of adjust Wallace coefficient were found with followed combinations: PFGE to predict MLST types = 100%, PFGE to predict blaOXA-51 SBT = 100%, blaOXA-51 SBT to predict MLST = 100%, MLST to predict blaOXA-51 SBT = 84.7%, rep-PCR to predict MLST = 81.5%, PFGE to predict rep-PCR = 69% and rep-PCR to predict blaOXA-51 SBT = 67.2%. PFGE and MLST are gold standard methods for outbreaks investigation and population structure studies respectively. Otherwise, these two techniques are technically, time and cost demanding. We recommend the use of blaOXA-51 SBT as first typing method to screen isolates and assign them to their corresponding clonal lineages. Repetitive sequence-based PCR is a rapid tool to access outbreaks but careful interpretation of results must be always performed.
Collapse
Affiliation(s)
- Rayane Rafei
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, Angers cedex, France
- Laboratoire de Santé et environnement, Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Fouad Dabboussi
- Laboratoire de Santé et environnement, Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Monzer Hamze
- Laboratoire de Santé et environnement, Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | - Matthieu Eveillard
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, Angers cedex, France
| | - Carole Lemarié
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, Angers cedex, France
| | - Marie-Pierre Gaultier
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, Angers cedex, France
| | - Hassan Mallat
- Laboratoire de Santé et environnement, Centre AZM pour la recherche en Biotechnologie et ses applications, Université Libanaise, Tripoli, Liban
| | | | - Rola Husni-Samaha
- Division of Infectious Diseases, Department of Internal Medicine, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Marie-Laure Joly-Guillou
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, Angers cedex, France
| | - Marie Kempf
- L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène, UPRES EA3142, Institut de Biologie en Santé – IRIS, CHU, Angers cedex, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU, Angers cedex, France
- * E-mail:
| |
Collapse
|
27
|
Lin MF, Lan CY. Antimicrobial resistance in Acinetobacter baumannii: From bench to bedside. World J Clin Cases 2014; 2:787-814. [PMID: 25516853 PMCID: PMC4266826 DOI: 10.12998/wjcc.v2.i12.787] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 08/25/2014] [Accepted: 10/27/2014] [Indexed: 02/05/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is undoubtedly one of the most successful pathogens in the modern healthcare system. With invasive procedures, antibiotic use and immunocompromised hosts increasing in recent years, A. baumannii has become endemic in hospitals due to its versatile genetic machinery, which allows it to quickly evolve resistance factors, and to its remarkable ability to tolerate harsh environments. Infections and outbreaks caused by multidrug-resistant A. baumannii (MDRAB) are prevalent and have been reported worldwide over the past twenty or more years. To address this problem effectively, knowledge of species identification, typing methods, clinical manifestations, risk factors, and virulence factors is essential. The global epidemiology of MDRAB is monitored by persistent surveillance programs. Because few effective antibiotics are available, clinicians often face serious challenges when treating patients with MDRAB. Therefore, a deep understanding of the resistance mechanisms used by MDRAB can shed light on two possible strategies to combat the dissemination of antimicrobial resistance: stringent infection control and antibiotic treatments, of which colistin-based combination therapy is the mainstream strategy. However, due to the current unsatisfying therapeutic outcomes, there is a great need to develop and evaluate the efficacy of new antibiotics and to understand the role of other potential alternatives, such as antimicrobial peptides, in the treatment of MDRAB infections.
Collapse
|
28
|
Chen CH, Huang CC. Tracing the emergence of multidrug-resistant Acinetobacter baumannii in a Taiwanese hospital by evaluating the presence of integron gene intI1. J Negat Results Biomed 2014; 13:15. [PMID: 25123361 PMCID: PMC4155391 DOI: 10.1186/1477-5751-13-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 08/08/2014] [Indexed: 11/16/2022] Open
Abstract
Background In Changhua County, Taiwan, the number of clinical Acinetobacter baumannii isolates has risen since 2002, and multidrug-resistant Acinetobacter baumannii (MDRAB) has spread rapidly throughout Taiwan. In this study, to reveal the mechanism involved with the rapid dissemination of MDRAB emergence, the utility of the class 1 integron, intI1 integrase gene, as an MDRAB-associated biomarker was examined. A cross-sectional, clinical epidemiological study was performed at Changhua Christian Hospital between January 1st, 2001 and December 31st, 2004. Besides the existence of intI1 gene was examined, the pulse-field gel electrophoresis (PFGE) was also performed to determine the epidemiological characteristics of the isolates. Findings The overall hospital infection rate was 5–6%, while the infection rate of the intensive care unit (ICU) fluctuated. No positive correlation was observed between MDRAB isolates and the presence of intI1 (r = 0.168, P = 0.254). Additionally, no positive correlation was observed between the infection rate in the ICU and the presence of intI1 (r = -0.107, P = 0.468) or between the hospital infection rate and the presence of intI1 (r = -0.189, P = 0.199). However, two predominant clones among the MDRAB isolates were identified by PFGE. Conclusions Although the presence of the intI1 gene does not seem suitable for tracing MDRAB emergence in Changhua County, two predominant clones were identified by PFGE, and subsequent studies to identify whether these clones were responsible for original nosocomial infection are needed.
Collapse
Affiliation(s)
| | - Chieh-Chen Huang
- College of Life Science, National Chung Hsing University, 250 Kuo-Kuang Road, Taichung 402, Taiwan.
| |
Collapse
|
29
|
Merabishvili M, Vandenheuvel D, Kropinski AM, Mast J, De Vos D, Verbeken G, Noben JP, Lavigne R, Vaneechoutte M, Pirnay JP. Characterization of newly isolated lytic bacteriophages active against Acinetobacter baumannii. PLoS One 2014; 9:e104853. [PMID: 25111143 PMCID: PMC4128745 DOI: 10.1371/journal.pone.0104853] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/18/2014] [Indexed: 12/24/2022] Open
Abstract
Based on genotyping and host range, two newly isolated lytic bacteriophages, myovirus vB_AbaM_Acibel004 and podovirus vB_AbaP_Acibel007, active against Acinetobacter baumannii clinical strains, were selected from a new phage library for further characterization. The complete genomes of the two phages were analyzed. Both phages are characterized by broad host range and essential features of potential therapeutic phages, such as short latent period (27 and 21 min, respectively), high burst size (125 and 145, respectively), stability of activity in liquid culture and low frequency of occurrence of phage-resistant mutant bacterial cells. Genomic analysis showed that while Acibel004 represents a novel bacteriophage with resemblance to some unclassified Pseudomonas aeruginosa phages, Acibel007 belongs to the well-characterized genus of the Phikmvlikevirus. The newly isolated phages can serve as potential candidates for phage cocktails to control A. baumannii infections.
Collapse
Affiliation(s)
- Maia Merabishvili
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
- Laboratory for Bacteriology Research (LBR), Faculty Medicine & Health Sciences, Ghent University, Ghent, Belgium
- * E-mail:
| | - Dieter Vandenheuvel
- Laboratory of Gene Technology, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Andrew M. Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jan Mast
- Electron Microscopy Unit, Veterinary and Agrochemical Research Centre, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
| | - Jean-Paul Noben
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mario Vaneechoutte
- Laboratory for Bacteriology Research (LBR), Faculty Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
| |
Collapse
|
30
|
Pasanen T, Koskela S, Mero S, Tarkka E, Tissari P, Vaara M, Kirveskari J. Rapid molecular characterization of Acinetobacter baumannii clones with rep-PCR and evaluation of carbapenemase genes by new multiplex PCR in Hospital District of Helsinki and Uusimaa. PLoS One 2014; 9:e85854. [PMID: 24465749 PMCID: PMC3897539 DOI: 10.1371/journal.pone.0085854] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 12/02/2013] [Indexed: 12/25/2022] Open
Abstract
Multidrug-resistant Acinetobacter baumannii (MDRAB) is an increasing problem worldwide. Prevalence of carbapenem resistance in Acinetobacter spp. due to acquired carbapenemase genes is not known in Finland. The purpose of this study was to examine prevalence and clonal spread of multiresistant A. baumannii group species, and their carbapenemase genes. A total of 55 Acinetobacter isolates were evaluated with repetitive PCR (DiversiLab) to analyse clonality of isolates, in conjunction with antimicrobial susceptibility profile for ampicillin/sulbactam, colistin, imipenem, meropenem, rifampicin and tigecycline. In addition, a new real-time PCR assay, detecting most clinically important carbapenemase genes just in two multiplex reactions, was developed. The assay detects genes for KPC, VIM, IMP, GES-1/-10, OXA-48, NDM, GIM-1, SPM-1, IMI/NMC-A, SME, CMY-10, SFC-1, SIM-1, OXA-23-like, OXA-24/40-like, OXA-58 and ISAbaI-OXA-51-like junction, and allows confident detection of isolates harbouring acquired carbapenemase genes. There was a time-dependent, clonal spread of multiresistant A. baumannii strongly correlating with carbapenamase gene profile, at least in this geographically restricted study material. The new carbapenemase screening assay was able to detect all the genes correctly suggesting it might be suitable for epidemiologic screening purposes in clinical laboratories.
Collapse
Affiliation(s)
- Tanja Pasanen
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
- * E-mail:
| | - Suvi Koskela
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Sointu Mero
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Eveliina Tarkka
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Päivi Tissari
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Martti Vaara
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Juha Kirveskari
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| |
Collapse
|
31
|
Lin MF, Liou ML, Tu CC, Yeh HW, Lan CY. Molecular epidemiology of integron-associated antimicrobial gene cassettes in the clinical isolates of Acinetobacter baumannii from northern Taiwan. Ann Lab Med 2013; 33:242-7. [PMID: 23826559 PMCID: PMC3698301 DOI: 10.3343/alm.2013.33.4.242] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/14/2013] [Accepted: 04/08/2013] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The aims of this study were to understand the molecular epidemiology of integron-associated gene cassettes in Acinetobacter baumannii across four hospitals in northern Taiwan and to clarify the relationship between the presence of integrons and antibiotic-resistant phenotypes. METHODS Sixty-five A. baumannii isolates, collected from the patients of four regional hospitals in northern Taiwan in 2009, were tested for the presence of integrons and their associated gene cassettes. The susceptibility difference between integron-positive and integron-negative A. baumannii strains was analyzed. Antibiotic-resistant phenotypes among A. baumannii with different types of gene cassette array combinations were also compared. RESULTS Around 72% of the A. baumannii isolates carried class 1 integrase genes. Despite this, only three gene cassette arrays were found in the integrons. Integron-positive strains were significantly more resistant to all the tested antibiotics than the integrase-negative strains. All the four types of A. baumannii with different gene cassette array combinations were multidrug-resistant in nature. Gene cassette array aacA4-catB8-aadA1 existed in all the integron-positive A. baumannii isolates. Repetitive-sequence-based PCR (rep-PCR) results revealed the prevalence of one major cluster of imipenem-resistant A. baumannii strains (84%) in the four regional hospitals. CONCLUSIONS The presence of integrons with associated antimicrobial resistance gene cassettes can be used as a representative marker of multidrug resistance in A. baumannii. Some prevalent gene cassette arrays may exist among epidemiologically unrelated A. baumannii strains.
Collapse
Affiliation(s)
- Ming-Feng Lin
- Department of Medicine, National Taiwan University Hospital Chu-Tung Branch, Hsin-Chu County, Taiwan
| | | | | | | | | |
Collapse
|
32
|
Lukinmaa-Åberg S, Horsma J, Pasanen T, Mero S, Aulu L, Vaara M, Siitonen A, Antikainen J. Applicability of DiversiLab repetitive sequence-based PCR method in epidemiological typing of enterohemorrhagic Escherichia coli (EHEC). Foodborne Pathog Dis 2013; 10:632-8. [PMID: 23692078 DOI: 10.1089/fpd.2012.1411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) causes diarrhea, often with severe complications. Rapid and discriminatory typing of EHEC using advanced molecular methods is needed for determination of the genetic relatedness of clones responsible for foodborne outbreaks and for finding out the transmission sources of the outbreaks. This study evaluated the potential of DiversiLab, a semiautomated repetitive sequence-based polymerase chain reaction method for the genotyping of EHEC strains. A set of 52 EHEC strains belonging to 15 O:H serotypes was clustered into 10 DiversiLab groups. All of the O157 strains and one O55 strain were classified into the same group based on a 90% similarity threshold. The other serotypes were classified to their own DiversiLab group, with the exception of one R:H(-) strain that was grouped with O5:H(-) strains. In addition, O26 and O111 strains were grouped together but ultimately subdivided according to their O-serotypes based on a 95% similarity threshold. The O104 strain, which was associated with a major outbreak of hemolytic uremic syndrome in Germany in May 2011, was also classified independently. The DiversiLab performed well in identifying isolates, but the discriminatory power of the repetitive sequence-based polymerase chain reaction method was lower than that of pulsed-field gel electrophoresis. Analysis of 15 enteropathogenic E. coli (EPEC) strains revealed that some EPEC strains clustered together with EHEC strains. Therefore, the DiversiLab system cannot be used to discriminate between these pathogroups. In conclusion, DiversiLab is a rapid and easy system for the primary exclusion of unrelated EHEC strains based on their serotypes, but more discriminatory methods, such as pulsed-field gel electrophoresis, are needed for accurate typing of the EHEC strains.
Collapse
Affiliation(s)
- Susanna Lukinmaa-Åberg
- Bacteriology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare THL, Helsinki, Finland
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Typing of nosocomial outbreaks of Acinetobacter baumannii by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2012; 51:603-6. [PMID: 23175257 DOI: 10.1128/jcm.01811-12] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been evaluated for the identification of multidrug-resistant Acinetobacter baumannii nosocomial outbreaks in comparison with the repetitive sequence-based PCR DiversiLab system. The results suggest that MALDI-TOF MS can be used for real-time detection of Acinetobacter outbreaks before results from DNA-based systems are available.
Collapse
|
34
|
Development and evaluation of a novel, semiautomated Clostridium difficile typing platform. J Clin Microbiol 2012; 51:621-4. [PMID: 23175261 DOI: 10.1128/jcm.02627-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe a novel, semiautomated Clostridium difficile typing platform that is based on PCR-ribotyping in conjunction with a semiautomated molecular typing system. The platform is reproducible with minimal intra- or interassay variability. This method exhibited a discriminatory index of 0.954 and is therefore comparable to more arduous typing systems, such as pulsed-field gel electrophoresis.
Collapse
|
35
|
Molecular epidemiology of Acinetobacter baumannii bloodstream isolates obtained in the United States from 1995 to 2004 using rep-PCR and multilocus sequence typing. J Clin Microbiol 2012; 50:3493-500. [PMID: 22895032 DOI: 10.1128/jcm.01759-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Using a repetitive-sequence-based (rep)-PCR (DiversiLab), we have molecularly typed Acinetobacter nosocomial bloodstream isolates (Acinetobacter baumannii [n = 187], Acinetobacter pittii [n = 23], and Acinetobacter nosocomialis [n = 61]) obtained from patients hospitalized in U.S. hospitals over a 10-year period (1995-2004) during a nationwide surveillance study (Surveillance and Control of Pathogens of Epidemiological Importance [SCOPE]). Patterns of A. baumannii rep-PCR were compared to those of previously identified international clonal lineages (ICs) and were further investigated by multilocus sequence typing (MLST) to compare the two typing methods. Forty-seven of the A. baumannii isolates clustered with the previously defined IC 2. ICs 1, 3, 6, and 7 were also detected. The remaining 81 isolates were unrelated to the described ICs. In contrast, A. pittii and A. nosocomialis isolates were more heterogeneous, as determined by rep-PCR. Our MLST results were in good correlation with the rep-PCR clusters. Our study confirms previous data indicating the predominance of a few major clonal A. baumannii lineages in the United States, particularly IC 2. The presence in the United States of A. baumannii ICs 1, 2, and 3 from as early as 1995 suggests that global dissemination of these lineages was an early event.
Collapse
|
36
|
Sibley CD, Peirano G, Church DL. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. INFECTION GENETICS AND EVOLUTION 2012; 12:505-21. [PMID: 22342514 PMCID: PMC7106020 DOI: 10.1016/j.meegid.2012.01.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/25/2022]
Abstract
Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.
Collapse
Affiliation(s)
- Christopher D. Sibley
- Department of Microbiology, Immunology & Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
| | - Deirdre L. Church
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Department of Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
- Corresponding author. Address: c/o Calgary Laboratory Services, 9-3535 Research Rd. N.W., Calgary, Alta, Canada T2L 2K8. Tel.: +1 403 770 3281; fax: +1 403 770 3347.
| |
Collapse
|