51
|
Khodayary R, Nikokar I, Mobayen MR, Afrasiabi F, Araghian A, Elmi A, Moradzadeh M. High incidence of type III secretion system associated virulence factors (exoenzymes) in Pseudomonas aeruginosa isolated from Iranian burn patients. BMC Res Notes 2019; 12:28. [PMID: 30646938 PMCID: PMC6334392 DOI: 10.1186/s13104-019-4071-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/11/2019] [Indexed: 01/09/2023] Open
Abstract
Objective The present study aimed to determine the prevalence of virulence factors and antimicrobial resistance profile of Pseudomonas aeruginosa strains isolated from Iranian burn patients. Results This cross-sectional study performed on 100 P. aeruginosa isolates which were recovered from burn wound specimens in 2014–2015. All presumptive isolates were identified by standard microbiologic tests. Antimicrobial susceptibility test was carried out by disk diffusion method. The presence of virulence genes was determined by PCR method. Antibiotic susceptibility results revealed that the isolates were mostly susceptible to amikacin (61%), ceftazidime (60%), and imipenem (55%). Moreover, 59% of the isolates were multi-drug resistance (MDR). The most prevalent MDR pattern was aminoglycosides–penicillins–fluoroquinolones–carbapenems (15%). The presence of exoT, exoY, exoS and exoU genes was detected in 100%, 100%, 59%, and 41% of the tested isolates, respectively. Results points out the pattern of MDR and genetic diversity of type III secretion system among P. aeruginosa strains isolated from the burn population. Overall, the association of MDR and the presence of the specific virulence genes can be a predictive marker for the persistence of these isolates in the hospitals and subsequently a worse clinical condition for the affected patients.
Collapse
Affiliation(s)
- Ramin Khodayary
- Department of Microbiology, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Iraj Nikokar
- Department of Microbiology, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran. .,Medical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran. .,Laboratory of Microbiology and Immunology of Infectious Diseases, Paramedicine Faculty, Guilan University of Medical Sciences, P.O. Box: 44715-1361, Langeroud, IR, Iran.
| | | | - Farhad Afrasiabi
- Department of Microbiology, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Afshin Araghian
- Medical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ali Elmi
- Medical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Meisam Moradzadeh
- Department of Microbiology, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| |
Collapse
|
52
|
Maria de Souza Morais S, Ferreira Rodigues N, Ingrid Oliveira da Silva N, Aparecido Salvador E, Rodrigues Franco I, Augusto Pires de Souza G, Henrique Cruvinel da Silva P, Gustavo Nogueira de Almeida L, Prado Rocha R, Carolina Toledo da Cunha Pereira A, Portela Ferreira G, Veras Quelemes P, Pereira de Araújo M, Fornias Sperandio F, Júnia de Souza Santos L, Assis Martins Filho O, Cosme Cotta Malaquias L, Felipe Leomil Coelho L. Serum albumin nanoparticles vaccine provides protection against a lethal Pseudomonas aeruginosa challenge. Vaccine 2018; 36:6408-6415. [DOI: 10.1016/j.vaccine.2018.08.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/18/2018] [Accepted: 08/29/2018] [Indexed: 12/31/2022]
|
53
|
Tap out: reducing waterborne Pseudomonas aeruginosa transmission in an intensive care unit. J Hosp Infect 2018; 102:75-81. [PMID: 30071267 DOI: 10.1016/j.jhin.2018.07.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Pseudomonas aeruginosa is a ubiquitous and important opportunistic pathogen in immunocompromised or critically ill patients. Nosocomial P. aeruginosa outbreaks have been associated with hospital water sources. AIM To describe engineering interventions to minimize contamination of water outlets and the subsequent clinical impact. METHODS New tap outlets were fitted at selected outlets across the intensive care unit (ICU). Laboratory testing demonstrated that, following artificial contamination with P. aeruginosa, these taps could be effectively decontaminated using a thermal washer-disinfector. Water samples were collected weekly from new outlets on the ICU over an eight-month period and tested for the enumeration of P. aeruginosa via membrane filtration. Surveillance of P. aeruginosa from clinical specimens was routinely undertaken. FINDINGS Prior to the interventions, water sampling on ICU indicated that 30% of the outlets were positive for P. aeruginosa at any one time, and whole genome sequencing data suggested at least 30% transmission from water to patient. Since their installation, weekly sampling of the new tap outlets has been negative for P. aeruginosa, and the number of P. aeruginosa clinical isolates has fallen by 50%. CONCLUSION Installation and maintenance of tap outlets free of P. aeruginosa can substantially reduce the number of P. aeruginosa clinical isolates in an ICU.
Collapse
|
54
|
Nayar G, Darley ESR, Hammond F, Matthews S, Turton J, Wach R. Does screening neonates in the neonatal intensive care unit for Pseudomonas aeruginosa colonization help prevent infection? J Hosp Infect 2018; 100:54-59. [PMID: 29964100 DOI: 10.1016/j.jhin.2018.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/22/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa (PA) is a Gram-negative environmental organism that can cause severe infection in immunosuppressed patients, including preterm neonates. In recent years, it has become common practice to screen neonates for PA colonization. AIM To assess the value of screening neonates for PA in (1) predicting the risk of developing severe PA infection and (2) directing infection control practice. METHODS Between August 2012 and September 2015, babies admitted to the neonatal intensive care unit (NICU) at North Bristol NHS Trust were screened routinely for PA colonization on admission and weekly thereafter. Data were also collected on babies who developed PA infection. Environmental samples from the NICU were tested for the presence of PA. Variable number tandem repeat (VNTR) typing was performed on all strains of PA from babies and the environment. FINDINGS No babies with positive screens subsequently developed PA infection. There was no VNTR strain evidence supporting cross-infection from the environment or other babies. CONCLUSION Screening neonates for PA did not identify babies who subsequently developed PA infection. Following cessation of screening in September 2015, there was no increase in the number of babies identified with PA infection.
Collapse
Affiliation(s)
- G Nayar
- Severn Pathology Infection Sciences, North Bristol NHS Trust, Bristol, UK.
| | - E S R Darley
- Severn Pathology Infection Sciences, North Bristol NHS Trust, Bristol, UK
| | - F Hammond
- Infection Prevention and Control, North Bristol NHS Trust, Bristol, UK
| | - S Matthews
- Infection Prevention and Control, North Bristol NHS Trust, Bristol, UK
| | - J Turton
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, Colindale, London, UK
| | - R Wach
- Neonatal Intensive Care, North Bristol NHS Trust, Bristol, UK
| |
Collapse
|
55
|
Chen JW, Lau YY, Krishnan T, Chan KG, Chang CY. Recent Advances in Molecular Diagnosis of Pseudomonasaeruginosa Infection by State-of-the-Art Genotyping Techniques. Front Microbiol 2018; 9:1104. [PMID: 29892277 PMCID: PMC5985333 DOI: 10.3389/fmicb.2018.01104] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/08/2018] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is a rod-shaped Gram-negative bacterium which is notably known as a pathogen in humans, animals, and plants. Infections caused by P. aeruginosa especially in hospitalized patients are often life-threatening and rapidly increasing worldwide throughout the years. Recently, multidrug-resistant P. aeruginosa has taken a toll on humans' health due to the inefficiency of antimicrobial agents. Therefore, the rapid and advanced diagnostic techniques to accurately detect this bacterium particularly in clinical samples are indeed necessary to ensure timely and effective treatments and to prevent outbreaks. This review aims to discuss most recent of state-of-the-art molecular diagnostic techniques enabling fast and accurate detection and identification of P. aeruginosa based on well-developed genotyping techniques, e.g., polymerase chain reaction, pulse-field gel electrophoresis, and next generation sequencing. The advantages and limitations of each of the methods are also reviewed.
Collapse
Affiliation(s)
- Jian-Woon Chen
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yin Yin Lau
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Thiba Krishnan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Chien-Yi Chang
- School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom
| |
Collapse
|
56
|
The Microbial Endocrinology of Pseudomonas aeruginosa: Inflammatory and Immune Perspectives. Arch Immunol Ther Exp (Warsz) 2018. [PMID: 29541797 DOI: 10.1007/s00005-018-0510-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Pseudomonas aeruginosa is a major pathogen responsible for both acute and chronic infection. Known as a colonising pathogen of the cystic fibrosis (CF) lung, it is implicated in other settings such as bronchiectasis. It has the ability to cause acute disseminated or localised infection particularly in the immunocompromised. Human hormones have been highlighted as potential regulators of bacterial virulence through crosstalk between analogous "quorum sensing" (QS) systems present in the bacteria that respond to mammalian hormones. Pseudomonas aeruginosa is known to utilise interconnected QS systems to coordinate its virulence and evade various aspects of the host immune system activated in response to infection. Several human hormones demonstrate an influence on P. aeruginosa growth and virulence. This inter-kingdom signalling, termed "microbial endocrinology" has important implications for host-microbe interaction during infection and, potentially opens up novel avenues for therapeutic intervention. This phenomenon, supported by the existence of sexual dichotomies in both microbial infection and chronic lung diseases such as CF is potentially explained by sex hormones and their influence on the infective process. This review summarises our current understanding of the microbial endocrinology of P. aeruginosa, including its endogenous QS systems and their intersection with human endocrinology, pathogenesis of infection and the host immune system.
Collapse
|
57
|
Kossow A, Kampmeier S, Willems S, Berdel WE, Groll AH, Burkhardt B, Rossig C, Groth C, Idelevich EA, Kipp F, Mellmann A, Stelljes M. Control of Multidrug-Resistant Pseudomonas aeruginosa in Allogeneic Hematopoietic Stem Cell Transplant Recipients by a Novel Bundle Including Remodeling of Sanitary and Water Supply Systems. Clin Infect Dis 2018; 65:935-942. [PMID: 28520856 DOI: 10.1093/cid/cix465] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/15/2017] [Indexed: 12/20/2022] Open
Abstract
Background Infections by multidrug-resistant Pseudomonas aeruginosa (MDRPa) are an important cause of morbidity and mortality in patients after allogeneic hematopoietic stem cell transplantation (HSCT). Humid environments can serve as a reservoir and source of infection by this pathogen. To minimize the risk of infection from these reservoirs, we performed extensive remodeling of sanitation and water installations as the focus of our hygiene bundle. Methods During the reconstruction of our transplantation unit (April 2011-April 2014) we implemented several technical modifications to reduce environmental contamination by and subsequent spreading of MDRPa, including a newly designed shower drain, disinfecting siphons underneath the sinks, and rimless toilets. During a 3-year study period (2012-2014), we tracked the number of patients affected by MDRPa (colonized and/or infected) and the outcome of infected patients, and monitored the environmental occurrence of this pathogen. We further performed whole-genome sequencing of nosocomial MDRPa strains to evaluate genotypic relationships between isolates. Results Whereas 31 (9.2%; 18 colonized, 13 infected) patients were affected in 2012 and 2013, the number decreased to 3 in 2014 (17%; 3 colonized, 0 infected). Lethality by MDRPa similarly decreased from 3.6% to 0%. Environmental detection of MDRPa decreased in toilets from 18.9% in 2012-2013 to 6.1% in the following year and from 8.1% to 3.0%, respectively, in shower outlets. Whole-genome sequencing showed close relationships between environmental and patient-derived isolates. Conclusions Hospital construction measures aimed at controlling environmental contamination by and spread of MDRPa are effective at minimizing the risk of highly lethal MDRPa infections.
Collapse
Affiliation(s)
| | | | | | | | - Andreas H Groll
- University Children's Hospital Muenster, Department of Pediatric Hematology and Oncology
| | - Birgit Burkhardt
- University Children's Hospital Muenster, Department of Pediatric Hematology and Oncology
| | - Claudia Rossig
- University Children's Hospital Muenster, Department of Pediatric Hematology and Oncology
| | | | | | | | | | | |
Collapse
|
58
|
Spalding C, Keen E, Smith DJ, Krachler AM, Jabbari S. Mathematical modelling of the antibiotic-induced morphological transition of Pseudomonas aeruginosa. PLoS Comput Biol 2018; 14:e1006012. [PMID: 29481562 PMCID: PMC5843380 DOI: 10.1371/journal.pcbi.1006012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/08/2018] [Accepted: 01/31/2018] [Indexed: 11/18/2022] Open
Abstract
Here we formulate a mechanistic mathematical model to describe the growth dynamics of P. aeruginosa in the presence of the β-lactam antibiotic meropenem. The model is mechanistic in the sense that carrying capacity is taken into account through the dynamics of nutrient availability rather than via logistic growth. In accordance with our experimental results we incorporate a sub-population of cells, differing in morphology from the normal bacillary shape of P. aeruginosa bacteria, which we assume have immunity from direct antibiotic action. By fitting this model to experimental data we obtain parameter values that give insight into the growth of a bacterial population that includes different cell morphologies. The analysis of two parameters sets, that produce different long term behaviour, allows us to manipulate the system theoretically in order to explore the advantages of a shape transition that may potentially be a mechanism that allows P. aeruginosa to withstand antibiotic effects. Our results suggest that inhibition of this shape transition may be detrimental to bacterial growth and thus suggest that the transition may be a defensive mechanism implemented by bacterial machinery. In addition to this we provide strong theoretical evidence for the potential therapeutic strategy of using antimicrobial peptides (AMPs) in combination with meropenem. This proposed combination therapy exploits the shape transition as AMPs induce cell lysis by forming pores in the cytoplasmic membrane, which becomes exposed in the spherical cells.
Collapse
Affiliation(s)
- Chloe Spalding
- School of Mathematics, University of Birmingham, Edgbaston Campus, Birmingham, United Kingdom
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, United Kingdom
| | - Emma Keen
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, United Kingdom
| | - David J. Smith
- School of Mathematics, University of Birmingham, Edgbaston Campus, Birmingham, United Kingdom
- Institute for Metabolism and Systems Research, University of Birmingham, Edgbaston Campus, Birmingham, United Kingdom
| | - Anne-Marie Krachler
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, Texas, United States of America
| | - Sara Jabbari
- School of Mathematics, University of Birmingham, Edgbaston Campus, Birmingham, United Kingdom
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, United Kingdom
| |
Collapse
|
59
|
Parcell BJ, Oravcova K, Pinheiro M, Holden MTG, Phillips G, Turton JF, Gillespie SH. Pseudomonas aeruginosa intensive care unit outbreak: winnowing of transmissions with molecular and genomic typing. J Hosp Infect 2017; 98:282-288. [PMID: 29229490 PMCID: PMC5840502 DOI: 10.1016/j.jhin.2017.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/03/2017] [Indexed: 12/29/2022]
Abstract
Background Pseudomonas aeruginosa healthcare outbreaks can be time consuming and difficult to investigate. Guidance does not specify which typing technique is most practical for decision-making. Aim To explore the usefulness of whole-genome sequencing (WGS) in the investigation of a P. aeruginosa outbreak, describing how it compares with pulsed-field gel electrophoresis (PFGE) and variable number tandem repeat (VNTR) analysis. Methods Six patient isolates and six environmental samples from an intensive care unit (ICU) positive for P. aeruginosa over two years underwent VNTR, PFGE and WGS. Findings VNTR and PFGE were required to fully determine the potential source of infection and rule out others. WGS results unambiguously distinguished linked isolates, giving greater assurance of the transmission route between wash-hand basin water and two patients, supporting the control measures employed. Conclusion WGS provided detailed information without the need for further typing. When allied to epidemiological information, WGS can be used to understand outbreak situations rapidly and with certainty. Implementation of WGS in real-time would be a major advance in day-to-day practice. It could become a standard of care as it becomes more widespread due to its reproducibility and lower costs.
Collapse
Affiliation(s)
- B J Parcell
- Ninewells Hospital & Medical School, Dundee, UK.
| | - K Oravcova
- School of Medicine, University of St Andrews, St Andrews, UK
| | - M Pinheiro
- School of Medicine, University of St Andrews, St Andrews, UK
| | - M T G Holden
- School of Medicine, University of St Andrews, St Andrews, UK
| | - G Phillips
- Ninewells Hospital & Medical School, Dundee, UK
| | - J F Turton
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, Colindale, UK
| | - S H Gillespie
- School of Medicine, University of St Andrews, St Andrews, UK
| |
Collapse
|
60
|
Hernández-Ramírez KC, Chávez-Jacobo VM, Valle-Maldonado MI, Patiño-Medina JA, Díaz-Pérez SP, Jácome-Galarza IE, Ortiz-Alvarado R, Meza-Carmen V, Ramírez-Díaz MI. Plasmid pUM505 encodes a Toxin-Antitoxin system conferring plasmid stability and increased Pseudomonas aeruginosa virulence. Microb Pathog 2017; 112:259-268. [PMID: 28970172 DOI: 10.1016/j.micpath.2017.09.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 12/19/2022]
Abstract
Pseudomonas aeruginosa plasmid pUM505 possesses a pathogenicity island that contains the pumAB genes that encode products with sequence similarity to Toxin-Antitoxin (TA) modules. RT-PCR assays on the overlapping regions of the pumAB genes generated a bicistronic messenger RNA, suggesting that they form an operon. When the pumAB genes were cloned into the pJET vector, recombinant plasmid pJET-pumAB was maintained under nonselective conditions in Escherichia coli cells after six daily subcultures, whereas pJET without pumAB genes was lost. These data indicate that pumAB genes confer post-segregational plasmid stability. In addition, overexpression of the PumA protein in the E. coli BL21 strain resulted in a significant growth inhibition, while BL21 co-expressing the PumA and PumB proteins did not show growth inhibition. These results indicate that pumAB genes encode a TA system where the PumB protein counters the toxic effects of the PumA toxin. Furthermore, P. aeruginosa PAO1 transformants with the pumA gene increased Caenorhabditis elegans and mouse mortality rate and improved mouse organ invasion, effects neutralized by the PumB protein. Moreover, purified recombinant His-PumA protein decreased the viability of C. elegans, indicating that the PumA protein could acts as a toxin. These results indicate that PumA has the potential to promoter the PAO1 virulence against C. elegans and mice when is expressed in absence of PumB. This is the first description, to our knowledge, of a plasmid-encoded TA system that confers plasmid stability and encoded a toxin with the possible ability to increase the P. aeruginosa virulence.
Collapse
Affiliation(s)
- K C Hernández-Ramírez
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - V M Chávez-Jacobo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - M I Valle-Maldonado
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - J A Patiño-Medina
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - S P Díaz-Pérez
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - I E Jácome-Galarza
- Laboratorio Estatal de Salud Pública, Secretaría de Salud Michoacán, Morelia, Mexico
| | - R Ortiz-Alvarado
- Facultad de Químico-Farmacobiología, Universidad Michoacana, Morelia, Mexico
| | - V Meza-Carmen
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - M I Ramírez-Díaz
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico.
| |
Collapse
|
61
|
Molecular epidemiology, resistance, and virulence properties of Pseudomonas aeruginosa cross-colonization clonal isolates in the non-outbreak setting. INFECTION GENETICS AND EVOLUTION 2017; 55:288-296. [PMID: 28911852 DOI: 10.1016/j.meegid.2017.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/08/2017] [Accepted: 09/09/2017] [Indexed: 12/15/2022]
Abstract
Pseudomonas aeruginosa is the predominant opportunistic pathogen leading to nosocomial infection and outbreak in hospitals. Hospitalized patients may be infected with this bacterium through close contact with contaminated environmental media. However, the molecular epidemiology, resistance, and virulence properties of Pseudomonas aeruginosa cross-colonization isolates has received limited attention in the non-outbreak setting. This study aims to investigate the epidemiological relationship of clinical and environmental P. aeruginosa isolates and to characterize the resistance and virulence properties of clonal clusters and sporadic strains in a non-outbreak setting. A total of 436 patients were screened for P. aeruginosa during hospitalization, and environmental samples were taken from their immediate ward media, including faucets, doorknobs, bedrails, pillows, quilts, and mattresses. As a result, 100 P. aeruginosa isolates were obtained, including 74 clinical strains and 26 environmental strains. By using Pulsed-Field Gel Electrophoresis, the fingerprint displayed 20 distinct clusters and 44 sporadic strains. According to identical genotypes, there were clear P. aeruginosa cross-colonization processes from the ward media to inpatients, indicating faucets, bedrails, and pillows as the main propagation media that had been contaminated by clonal isolates previously detected in other patients. In addition, there were P. aeruginosa transmission processes between inpatients that were unexplained for lack of epidemiological evidence. As compared to sporadic strains of P. aeruginosa, clonal clusters are more capable of producing high-level biofilm, developing multi-drug resistance and inducing high-degree cytotoxicity. Among P. aeruginosa clonal clusters, there was a strong positive correlation between antibiotic resistance and biofilm production. We conclude that constant cross-colonization of P. aeruginosa clonal isolates will pose a long-term serious threat in terms of nosocomial outbreaks. Thus, strict disinfection and sterilization procedures should be implemented for ward media, and P. aeruginosa in environments and patients should be closely monitored, especially those strains with strong resistance and virulence.
Collapse
|
62
|
Lalancette C, Charron D, Laferrière C, Dolcé P, Déziel E, Prévost M, Bédard E. Hospital Drains as Reservoirs of Pseudomonas aeruginosa: Multiple-Locus Variable-Number of Tandem Repeats Analysis Genotypes Recovered from Faucets, Sink Surfaces and Patients. Pathogens 2017; 6:pathogens6030036. [PMID: 28792484 PMCID: PMC5617993 DOI: 10.3390/pathogens6030036] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 12/16/2022] Open
Abstract
Identifying environmental sources of Pseudomonas aeruginosa (Pa) related to hospital-acquired infections represents a key challenge for public health. Biofilms in water systems offer protection and favorable growth conditions, and are prime reservoirs of microorganisms. A comparative genotyping survey assessing the relationship between Pa strains recovered in hospital sink biofilm and isolated in clinical specimens was conducted. Environmental strains from drain, faucet and sink-surface biofilm were recovered by a culture method after an incubation time ranging from 48 to 240 h. The genotyping of 38 environmental and 32 clinical isolates was performed using a multiple-locus variable-number of tandem repeats analysis (MLVA). More than one-third of Pa isolates were only cultivable following ≥48 h of incubation, and were predominantly from faucet and sink-surface biofilms. In total, 41/70 strains were grouped within eight genotypes (A to H). Genotype B grouped a clinical and an environmental strain isolated in the same ward, 5 months apart, suggesting this genotype could thrive in both contexts. Genotype E grouped environmental isolates that were highly prevalent throughout the hospital and that required a longer incubation time. The results from the multi-hospital follow-up study support the drain as an important reservoir of Pa dissemination to faucets, sink surfaces and patients. Optimizing the recovery of environmental strains will strengthen epidemiological investigations, facilitate pathway identification, and assist in identifying and controlling the reservoirs potentially associated to hospital-acquired infections.
Collapse
Affiliation(s)
| | - Dominique Charron
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada.
| | - Céline Laferrière
- Department of microbiology, infectious diseases and immunology, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Patrick Dolcé
- Department of Medical Microbiology and Infectious Diseases, Centre Hospitalier Régional de Rimouski, Rimouski, QC G5L 5T1, Canada.
| | - Eric Déziel
- INRS-Institut Armand-Frappier, Laval, QC H7V 1B7, Canada.
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada.
| | - Emilie Bédard
- INRS-Institut Armand-Frappier, Laval, QC H7V 1B7, Canada.
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada.
| |
Collapse
|
63
|
Abstract
Pseudomonas aeruginosa is an important nosocomial pathogen widely colonizing hospital water supplies. The Department of Health (England) Health Technical Memorandum (HTM) 04-01 addresses the risk posed by recommending water-testing in augmented care areas including outpatient haemodialysis. We discuss how two teaching hospitals independently reviewed the risk to outpatient haemodialysis patients, drawing the same conclusion. The highest number of infection episodes with P. aeruginosa was observed in critical care followed by burns and haematology, with the lowest in haemodialysis. Based on these results, we suggest that water sampling should be undertaken in areas such as critical care, burns, and haematology, but not in outpatient haemodialysis.
Collapse
|
64
|
Hutchins CF, Moore G, Thompson KA, Webb J, Walker JT. Contamination of hospital tap water: the survival and persistence of Pseudomonas aeruginosa on conventional and 'antimicrobial' outlet fittings. J Hosp Infect 2017; 97:156-161. [PMID: 28602704 DOI: 10.1016/j.jhin.2017.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/02/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa infections have been linked to contaminated hospital taps, highlighting the potential for tap outlet fittings (OF) to harbour biofilm. P. aeruginosa may be transferred to OFs via contaminated cleaning cloths. Suggested interventions include flushing regimens and alternative OF designs. AIM To investigate the transfer of P. aeruginosa from a contaminated cleaning cloth to conventional and 'antimicrobial/antibiofilm' OFs and to determine whether this contamination persists and/or leads to contamination of tap water. METHODS Microfibre cloths contaminated with P. aeruginosa (108 cfu/mL) were used to wipe four different types of OF [one of conventional design (OF-A) and three marketed as 'antimicrobial' and/or 'antibiofilm' (OF- B, -C and -D)]. OFs were inserted into an experimental water distribution system for up to 24 h. Survival was assessed by culture. Single and multiple water samples were collected and cultured for P. aeruginosa. FINDINGS The median number of P. aeruginosa transferred from cloth to OF was 5.7 × 105 cfu (OF-A), 1.9 × 106 cfu (OF-B), 1.4 × 105 cfu (OF-C) and 2.9 × 106 cfu (OF-D). Numbers declined on all OFs during the 24 h period with log reductions ranging from 3.5 (OF-C) to 5.2 (OF-B; P > 0.05). All water samples delivered immediately after OF contamination contained P. aeruginosa at ≥10 cfu per 100 mL. Contamination of water delivered from OF-A persisted despite continued flushing. Water delivered from OF-B did not contain P. aeruginosa beyond the first flush. CONCLUSION Contaminated cleaning cloths may transfer P. aeruginosa to OFs, leading to contamination of tap water. Although not removing the potential for contamination, 'antimicrobial/antibiofilm' OFs may prevent P. aeruginosa from continually contaminating water delivered from the outlet.
Collapse
Affiliation(s)
- C F Hutchins
- Biosafety, Air and Water Microbiology Group, Public Health England, Porton Down, UK; Centre for Biological Sciences, Faculty of Natural and Environmental Sciences and Institute for Life Sciences, University of Southampton, Southampton, UK.
| | - G Moore
- Biosafety, Air and Water Microbiology Group, Public Health England, Porton Down, UK
| | - K-A Thompson
- Biosafety, Air and Water Microbiology Group, Public Health England, Porton Down, UK
| | - J Webb
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - J T Walker
- Biosafety, Air and Water Microbiology Group, Public Health England, Porton Down, UK
| |
Collapse
|
65
|
Petitjean M, Martak D, Silvant A, Bertrand X, Valot B, Hocquet D. Genomic characterization of a local epidemic Pseudomonas aeruginosa reveals specific features of the widespread clone ST395. Microb Genom 2017; 3:e000129. [PMID: 29177088 PMCID: PMC5695207 DOI: 10.1099/mgen.0.000129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/23/2017] [Indexed: 12/21/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen with several clones being frequently associated with outbreaks in hospital settings. ST395 is among these so-called ‘international’ clones. We aimed here to define the biological features that could have helped the implantation and spread of the clone ST395 in hospital settings. The complete genome of a multidrug resistant index isolate (DHS01) of a large hospital outbreak was analysed. We identified DHS01-specific genetic elements, among which were identified those shared with a panel of six independent ST395 isolates responsible for outbreaks in other hospitals. DHS01 has the fifth largest chromosome of the species (7.1 Mbp), with most of its 1555 accessory genes borne by either genomic islands (GIs, n=48) or integrative and conjugative elements (ICEs, n=5). DHS01 is multidrug resistant mostly due to chromosomal mutations. It displayed signatures of adaptation to chronic infection in part due to the loss of a 131 kbp chromosomal fragment. Four GIs were specific to the clone ST395 and contained genes involved in metabolism (GI-4), in virulence (GI-6) and in resistance to copper (GI-7). GI-7 harboured an array of six copper transporters and was shared with non-pathogenic Pseudomonas sp. retrieved from copper-contaminated environments. Copper resistance was confirmed phenotypically in all other ST395 isolates and possibly accounted for the spreading capability of the clone in hospital outbreaks, where water networks have been incriminated. This suggests that genes transferred from copper-polluted environments may have favoured the implantation and spread of the international clone P. aeruginosa ST395 in hospital settings.
Collapse
Affiliation(s)
- Marie Petitjean
- 1Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France.,2UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Daniel Martak
- 1Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France.,2UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Alicia Silvant
- 1Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France
| | - Xavier Bertrand
- 1Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France.,2UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Benoit Valot
- 2UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Didier Hocquet
- 2UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France.,3Centre de Ressources Biologiques - Filière Microbiologique, Centre Hospitalier Universitaire de Besançon, 3 Boulevard Fleming, Besançon, France.,1Hygiène Hospitalière, Centre Hospitalier Régional Universitaire de Besançon, Besançon, France
| |
Collapse
|
66
|
Walker J, Moore G, Collins S, Parks S, Garvey MI, Lamagni T, Smith G, Dawkin L, Goldenberg S, Chand M. Microbiological problems and biofilms associated with Mycobacterium chimaera in heater-cooler units used for cardiopulmonary bypass. J Hosp Infect 2017; 96:209-220. [PMID: 28532976 DOI: 10.1016/j.jhin.2017.04.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/19/2017] [Indexed: 01/21/2023]
Abstract
The role of heater-cooler units (HCUs) in the transmission of Mycobacterium chimaera during open heart surgery has been recognized since 2013. Subsequent investigations uncovered a remarkable global outbreak reflecting the wide distribution of implicated devices. HCUs are an essential component of cardiopulmonary bypass operations and their withdrawal would severely affect capacity for life-saving cardiac surgery. However, studies have demonstrated that many HCUs are contaminated with a wide range of micro-organisms, including M. chimaera and complex biofilms. Whole genome sequencing of M. chimaera isolates recovered from one manufacturer's HCUs, worldwide, has demonstrated a high level of genetic similarity, for which the most plausible hypothesis is a point source contamination of the devices. Dissemination of bioaerosols through breaches in the HCU water tanks is the most likely route of transmission and airborne bacteria have been shown to have reached the surgical field even with the use of ultraclean theatre ventilation. Controlling the microbiological quality of the water circulating in HCUs and reducing biofilm formation has been a major challenge for many hospitals. However, enhanced decontamination strategies have been recommended by manufacturers, and, although they are not always effective in eradicating M. chimaera from HCUs, UK hospitals have not reported any new cases of M. chimaera infection since implementing these mitigation strategies. Water safety groups in hospitals should be aware that water in medical devices such as HCUs may act as a vector in the transmission of potentially fatal water-borne infections.
Collapse
Affiliation(s)
- J Walker
- Biosafety, Air and Water Microbiology Group, National Infection Service, Public Health England, Porton Down, Salisbury, UK.
| | - G Moore
- Biosafety, Air and Water Microbiology Group, National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - S Collins
- Biosafety, Air and Water Microbiology Group, National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - S Parks
- Biosafety, Air and Water Microbiology Group, National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - M I Garvey
- Infection Prevention and Control Team, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Edgbaston, Birmingham, UK
| | - T Lamagni
- Healthcare-Associated Infection & Antimicrobial Resistance Department, National Infection Service, Public Health England, Colindale, London, UK
| | - G Smith
- Public Health England National Mycobacterial Reference Service, Birmingham Public Health Laboratory, Birmingham, UK
| | - L Dawkin
- Estates and Facilities, University Hospitals Coventry and Warwickshire NHS Trust, Walsall, UK
| | - S Goldenberg
- Centre for Clinical Infection and Diagnostics Research, King's College, London and Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - M Chand
- Reference Microbiology, National Infection Service, Public Health England, Colindale, London, UK; Guy's & St Thomas' NHS Foundation Trust, London, UK; National Institute for Health Research, Health Protection Research Unit in Respiratory Infections, Imperial College, London, UK
| |
Collapse
|
67
|
Varin A, Valot B, Cholley P, Morel C, Thouverez M, Hocquet D, Bertrand X. High prevalence and moderate diversity of Pseudomonas aeruginosa in the U-bends of high-risk units in hospital. Int J Hyg Environ Health 2017; 220:880-885. [PMID: 28456381 DOI: 10.1016/j.ijheh.2017.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/02/2017] [Accepted: 04/09/2017] [Indexed: 11/15/2022]
Abstract
The presence of P. aeruginosa in water supply is clearly identified as a risk factor for P. aeruginosa infection in critical care units, even if routes of transmission are often unclear and remain a matter of debate. We determined here the frequency of U-bends contaminated with P. aeruginosa in high-risk units and described the population structure of this opportunistic pathogen in a non-outbreak situation. Eighty-seven U-bends from sinks of rooms in five wards were sampled 3 times and P. aeruginosa was detected in 121 of the 261 (46.4%) U-bend samples. We genotyped 123 P. aeruginosa isolates with pulsed-field gel electrophoresis and multilocus sequence typing and found 41 pulsotypes distributed in 21 Sequence Types (STs). Seven major ST (ST111, CC235, CC253, ST520, ST539, ST1216, and ST1725) were overrepresented in the collection, including the high-risk clones ST111, CC253, and CC235. The distribution of the 21 STs in the cladogram of the species was uneven with most major STs clustering into 2 clades. The major STs were found in different units and buildings and could be represented by a high diversity of pulsotypes. Altogether, this suggests a long term presence of P. aeruginosa in the hospital water network, possibly contaminated by the distribution water or by plumbing fittings before putting into service. Analysis of resistance rates showed that the deficiency of porin OprD was very frequent in U-bends isolates that may benefit from this resistance mechanism in hospital water fittings. In conclusion, our study demonstrates that U-bends of high-risk units are very frequently contaminated with P. aeruginosa with a moderate genomic diversity and with an over-representation of adapted clones.
Collapse
Affiliation(s)
- Amélie Varin
- Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Benoît Valot
- UMR 6249 Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Pascal Cholley
- Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Camille Morel
- Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Michelle Thouverez
- Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Didier Hocquet
- Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France; Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Xavier Bertrand
- Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France.
| |
Collapse
|
68
|
McCarthy KL, Kidd TJ, Paterson DL. Molecular epidemiology of Pseudomonas aeruginosa bloodstream infection isolates in a non-outbreak setting. J Med Microbiol 2017; 66:154-159. [PMID: 28260586 DOI: 10.1099/jmm.0.000413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
PURPOSE The molecular epidemiology of Pseudomonas aeruginosa bloodstream infection (BSI) isolates has received limited attention. This study aims to characterize the molecular relationship of P. aeruginosa BSI isolates in the non-outbreak setting at a single tertiary healthcare facility. METHODOLOGY P. aeruginosa BSI isolates from patients who were admitted to the Royal Brisbane and Women's Hospital over a 13 month period from November 2009 were identified retrospectively from the Pathology Queensland Clinical and Scientific Information System. The isolates were typed by the iPLEX MassARRAY matrix assisted lazer desorption/isonisation time of flight (MALDI-TOF) MS genotyping. The DiversiLab automated rapid strain typing platform (bioMérieux) was used to assess the genotypic relationships between study isolates that showed indistinguishable iPLEX20SNP profiles. Clinical data was also collected retrospectively from patient notes. RESULTS Fifty-three P. aeruginosa BSI episodes were available for study. Thirty-five different clones or clonal complexes were identified by the iPLEX MassARRAY MALDI-TOF MS genotyping. Seventeen BSI isolates with indistinguishable iPLEX20SNP profiles underwent further DiversiLab genotyping and were found to belong to a further 13 different genotypes. There was no relationship between clonality and acquisition type, source of infection or length of stay in the setting of hospital-acquired infection. CONCLUSION The non-clonal population structure suggests that there is ongoing environmental exposure of inpatients to P. aeruginosa. In clinical areas dealing with at-risk patients, routine attention to mechanism of environmental colonization is important and should be addressed even in the non-outbreak setting.
Collapse
Affiliation(s)
- Kate L McCarthy
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - Tim J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK.,Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - David L Paterson
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| |
Collapse
|
69
|
Infection control in the new age of genomic epidemiology. Am J Infect Control 2017; 45:170-179. [PMID: 28159067 DOI: 10.1016/j.ajic.2016.05.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/22/2016] [Accepted: 05/23/2016] [Indexed: 12/25/2022]
Abstract
With the growing importance of infectious diseases in health care and communicable disease outbreaks garnering increasing attention, new technologies are playing a greater role in helping us prevent health care-associated infections and provide optimal public health. The microbiology laboratory has always played a large role in infection control by providing tools to identify, characterize, and track pathogens. Recently, advances in DNA sequencing technology have ushered in a new era of genomic epidemiology, where traditional molecular diagnostics and genotyping methods are being enhanced and even replaced by genomics-based methods to aid epidemiologic investigations of communicable diseases. The ability to analyze and compare entire pathogen genomes has allowed for unprecedented resolution into how and why infectious diseases spread. As these genomics-based methods continue to improve in speed, cost, and accuracy, they will be increasingly used to inform and guide infection control and public health practices.
Collapse
|
70
|
Guthrie JL, Gardy JL. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Ann N Y Acad Sci 2016; 1388:59-77. [PMID: 28009051 DOI: 10.1111/nyas.13273] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022]
Abstract
Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission.
Collapse
Affiliation(s)
- Jennifer L Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.,Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| |
Collapse
|
71
|
Targeting bacterial adherence inhibits multidrug-resistant Pseudomonas aeruginosa infection following burn injury. Sci Rep 2016; 6:39341. [PMID: 27996032 PMCID: PMC5171828 DOI: 10.1038/srep39341] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/18/2016] [Indexed: 12/19/2022] Open
Abstract
Classical antimicrobial drugs target proliferation and therefore place microbes under extreme selective pressure to evolve resistance. Alternative drugs that target bacterial virulence without impacting survival directly offer an attractive solution to this problem, but to date few such molecules have been discovered. We previously discovered a widespread group of bacterial adhesins, termed Multivalent Adhesion Molecules (MAMs) that are essential for initial binding of bacteria to host tissues and virulence. Thus, targeting MAM-based adherence is a promising strategy for displacing pathogens from host tissues and inhibiting infection. Here, we show that topical application of polymeric microbeads functionalized with the adhesin MAM7 to a burn infected with multidrug-resistant Pseudomonas aeruginosa substantially decreased bacterial loads in the wound and prevented the spread of the infection into adjacent tissues. As a consequence, the application of this adhesion inhibitor allowed for vascularization and wound healing, and maintained local and systemic inflammatory responses to the burn. We propose that MAM7-functionalized microbeads can be used as a topical treatment, to reduce bacterial attachment and hence prevent bacterial colonization and infection of wounds. As adhesion is not required for microbial survival, this anti-infective strategy has the potential to treat multidrug-resistant infections and limit the emergence of drug-resistant pathogens.
Collapse
|
72
|
Advances in the Microbiome: Applications to Clostridium difficile Infection. J Clin Med 2016; 5:jcm5090083. [PMID: 27657145 PMCID: PMC5039486 DOI: 10.3390/jcm5090083] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/14/2022] Open
Abstract
Clostridium difficile is a major cause of morbidity and mortality worldwide, causing over 400,000 infections and approximately 29,000 deaths in the United States alone each year. C. difficile is the most common cause of nosocomial diarrhoea in the developed world, and, in recent years, the emergence of hyper-virulent (mainly ribotypes 027 and 078, sometimes characterised by increased toxin production), epidemic strains and an increase in the number of community-acquired infections has caused further concern. Antibiotic therapy with metronidazole, vancomycin or fidaxomicin is the primary treatment for C. difficile infection (CDI). However, CDI is unique, in that, antibiotic use is also a major risk factor for acquiring CDI or recurrent CDI due to disruption of the normal gut microbiota. Therefore, there is an urgent need for alternative, non-antibiotic therapeutics to treat or prevent CDI. Here, we review a number of such potential treatments which have emerged from advances in the field of microbiome research.
Collapse
|
73
|
Reichert F, Piening B, Geffers C, Gastmeier P, Bührer C, Schwab F. Pathogen-Specific Clustering of Nosocomial Blood Stream Infections in Very Preterm Infants. Pediatrics 2016; 137:peds.2015-2860. [PMID: 26956103 DOI: 10.1542/peds.2015-2860] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/05/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Nosocomial infections in NICUs tend to cluster, sometimes as devastating outbreaks, but pathogen-specific transmission probabilities are unknown. We aimed to quantify the pathogen-specific risk of a blood stream infection (BSI) in preterm infants after an index case with that pathogen in the same department. METHODS Data of 44 818 infants below 1500 g birth weight of the German NICU surveillance system (2000-2011) were used to calculate the probability of a BSI in the presence or absence of another infant in the same unit with a same-pathogen BSI. RESULTS The relative risk was similar for the more common pathogens, Enterococcus spp (4.3; 95% confidence interval: 2.7-6.9; n = 243), Enterobacter spp (7.9, 5.4-11.4; n = 246), Escherichia coli (7.9; 5.1-12.1; n = 210), Candida albicans (8.7; 5.0-15.4; n = 138), Staphylococcus aureus (9.5; 7.6-12.1; n = 407) and Klebsiella spp (13.1; 9.0-19.1; n = 190) but markedly elevated for Serratia spp (77.5; 41.1-146.1; n = 58) and Pseudomonas aeruginosa (64.5; 25.7-162.1; n = 38). Rates of BSI per 100 exposed infants ranged between 2.21 (Enterococcus) and 8.15 (Serratia). The same pattern emerged after adjustments were made for patients' characteristics or when the analysis was restricted to positive blood cultures during the preceding 30 days. CONCLUSIONS Although BSIs with P aeruginosa or Serratia spp in preterm infants are rare, they are associated with a markedly elevated risk of secondary same-pathogen BSI and should prompt intensified active surveillance and infection control measures.
Collapse
Affiliation(s)
| | - Brar Piening
- Institute for Hygiene and Environmental Medicine, Charité University Medical Center, Berlin, Germany
| | - Christine Geffers
- Institute for Hygiene and Environmental Medicine, Charité University Medical Center, Berlin, Germany
| | - Petra Gastmeier
- Institute for Hygiene and Environmental Medicine, Charité University Medical Center, Berlin, Germany
| | | | - Frank Schwab
- Institute for Hygiene and Environmental Medicine, Charité University Medical Center, Berlin, Germany
| |
Collapse
|
74
|
Kanamori H, Weber DJ, Rutala WA. Healthcare Outbreaks Associated With a Water Reservoir and Infection Prevention Strategies. Clin Infect Dis 2016; 62:1423-35. [DOI: 10.1093/cid/ciw122] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022] Open
|
75
|
Olga P, Apostolos V, Alexis G, George V, Athena M. Antibiotic resistance profiles of Pseudomonas aeruginosa isolated from various Greek aquatic environments. FEMS Microbiol Ecol 2016; 92:fiw042. [PMID: 26917780 DOI: 10.1093/femsec/fiw042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2016] [Indexed: 12/18/2022] Open
Abstract
A large number of antibiotic-resistant P. aeruginosa isolates are continuously discharged into natural water basins mainly through sewage. However, the environmental reservoirs of antibiotic resistance factors are poorly understood. In this study, the antibiotic resistance patterns of 245 isolates from various aquatic sites in Greece were analysed. Twenty-three isolates with resistance patterns cefotaxime-aztreonam-ceftazidime, cefotaxime-aztreonam-meropenem, cefotaxime-ceftazidime-meropenem, cefotaxime-ceftazidime-aztreonam-meropenem and cefotaxime-ceftazidime-cefepime-aztreonam-meropenem were screened phenotypically for the presence of extended spectrum β-lactamases (ESBLs), while 77 isolates with various resistant phenotypes were screened for the presence of class 1 and class 2 integrase genes. The aztreonam-resistant isolates and ESBL producers were the main resistant phenotypes in all habitats tested. In 13/77 isolates class 1 integron was detected, while all tested isolates were negative for the presence of the class 2 integrase gene. CTX-M group 9 β-lactamase was present in a small number of isolates (three isolates) highlighting the emergence of ESBL genes in aquatic environments. As a conclusion, it seems that Greek water bodies could serve as a potential reservoir of resistant P. aeruginosa isolates posing threats to human and animal health.
Collapse
Affiliation(s)
- Pappa Olga
- Central Public Health Laboratory, Hellenic Centre for Disease Control and Prevention, Athens, Greece Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece Department of Medical Laboratories Technological Educational Institute of Athens, Athens, Greece
| | - Vantarakis Apostolos
- Environmental Microbiology Unit, Department of Public Health, School of Medicine, University of Patras, Greece
| | - Galanis Alexis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Mavridou Athena
- Department of Medical Laboratories Technological Educational Institute of Athens, Athens, Greece
| |
Collapse
|
76
|
Raza S, Luheshi L. Big data or bust: realizing the microbial genomics revolution. Microb Genom 2016; 2:e000046. [PMID: 28348842 PMCID: PMC5320582 DOI: 10.1099/mgen.0.000046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 12/16/2015] [Indexed: 12/29/2022] Open
Abstract
Pathogen genomics has the potential to transform the clinical and public health management of infectious diseases through improved diagnosis, detection and tracking of antimicrobial resistance and outbreak control. However, the wide-ranging benefits of this technology can only fully be realized through the timely collation, integration and sharing of genomic and clinical/epidemiological metadata by all those involved in the delivery of genomic-informed services. As part of our review on bringing pathogen genomics into ‘health-service’ practice, we undertook extensive stakeholder consultation to examine the factors integral to achieving effective data sharing and integration. Infrastructure tailored to the needs of clinical users, as well as practical support and policies to facilitate the timely and responsible sharing of data with relevant health authorities and beyond, are all essential. We propose a tiered data sharing and integration model to maximize the immediate and longer term utility of microbial genomics in healthcare. Realizing this model at the scale and sophistication necessary to support national and international infection management services is not uncomplicated. Yet the establishment of a clear data strategy is paramount if failures in containing disease spread due to inadequate knowledge sharing are to be averted, and substantial progress made in tackling the dangers posed by infectious diseases.
Collapse
|
77
|
Luheshi LM, Raza S, Peacock SJ. Moving pathogen genomics out of the lab and into the clinic: what will it take? Genome Med 2015; 7:132. [PMID: 26719100 PMCID: PMC4697326 DOI: 10.1186/s13073-015-0254-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Pathogen genomic analysis is a potentially transformative new approach to the clinical and public-health management of infectious diseases. Health systems investing in this technology will need to build infrastructure and develop policies that ensure genomic information can be generated, shared and acted upon in a timely manner.
Collapse
Affiliation(s)
| | - Sobia Raza
- PHG Foundation, 2 Worts Causeway, Cambridge, CB1 8RN, UK.
| | - Sharon J Peacock
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| |
Collapse
|
78
|
Lee RS, Behr MA. The implications of whole-genome sequencing in the control of tuberculosis. Ther Adv Infect Dis 2015; 3:47-62. [PMID: 27034776 DOI: 10.1177/2049936115624630] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The availability of whole-genome sequencing (WGS) as a tool for the diagnosis and clinical management of tuberculosis (TB) offers considerable promise in the fight against this stubborn epidemic. However, like other new technologies, the best application of WGS remains to be determined, for both conceptual and technical reasons. In this review, we consider the potential value of WGS in the clinical laboratory for the detection of Mycobacterium tuberculosis and the prediction of antibiotic resistance. We also discuss issues pertaining to data generation, interpretation and dissemination, given that WGS has to date been generally performed in research labs where results are not necessarily packaged in a clinician-friendly format. Although WGS is far more accessible now than it was in the past, the transition from a research tool to study TB into a clinical test to manage this disease may require further fine-tuning. Improvements will likely come through iterative efforts that involve both the laboratories ready to move TB into the genomic era and the front-line clinical/public health staff who will be interpreting the results to inform management decisions.
Collapse
Affiliation(s)
- Robyn S Lee
- McGill University, Department of Epidemiology, Biostatistics and Occupational Health, The Research Institute of the McGill University Health Centre and McGill International TB Centre, Montreal, QC, Canada
| | | |
Collapse
|
79
|
Arnold C. Outbreak Breakthrough: Using Whole-Genome Sequencing to Control Hospital Infection. ENVIRONMENTAL HEALTH PERSPECTIVES 2015; 123:A281-A286. [PMID: 26523889 PMCID: PMC4629729 DOI: 10.1289/ehp.123-a281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
|
80
|
Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM, Cookson BT, Shendure J, Salipante SJ. A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota. PLoS Genet 2015; 11:e1005413. [PMID: 26230489 PMCID: PMC4521703 DOI: 10.1371/journal.pgen.1005413] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/02/2015] [Indexed: 01/05/2023] Open
Abstract
Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here, over the course of one year, we performed prospective collection and whole genome sequencing of nearly all bacterial isolates obtained from a tertiary care hospital's intensive care units (ICUs). This unbiased collection of 1,229 bacterial genomes from 391 patients enables detailed exploration of several features of clinical pathogens. A sizable fraction of isolates identified as clinically relevant corresponded to previously undescribed species: 12% of isolates assigned a species-level classification by conventional methods actually qualified as distinct, novel genomospecies on the basis of genomic similarity. Pan-genome analysis of the most frequently encountered pathogens in the collection revealed substantial variation in pan-genome size (1,420 to 20,432 genes) and the rate of gene discovery (1 to 152 genes per isolate sequenced). Surprisingly, although potential nosocomial transmission of actively surveilled pathogens was rare, 8.7% of isolates belonged to genomically related clonal lineages that were present among multiple patients, usually with overlapping hospital admissions, and were associated with clinically significant infection in 62% of patients from which they were recovered. Multi-patient clonal lineages were particularly evident in the neonatal care unit, where seven separate Staphylococcus epidermidis clonal lineages were identified, including one lineage associated with bacteremia in 5/9 neonates. Our study highlights key differences in the information made available by conventional microbiological practices versus whole genome sequencing, and motivates the further integration of microbial genome sequencing into routine clinical care.
Collapse
Affiliation(s)
- David J. Roach
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Joshua N. Burton
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Bethany Stackhouse
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Susan M. Butler-Wu
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Brad T. Cookson
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Stephen J. Salipante
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| |
Collapse
|
81
|
Whole Genome Sequencing in Real-Time Investigation and Management of a Pseudomonas aeruginosa Outbreak on a Neonatal Intensive Care Unit. Infect Control Hosp Epidemiol 2015; 36:1058-64. [PMID: 26050101 DOI: 10.1017/ice.2015.133] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVE To use whole genome sequencing to describe the likely origin of an outbreak of Pseudomonas aeruginosa in a neonatal unit. DESIGN Outbreak investigation. SETTING The neonatal intensive care unit service of a major obstetric tertiary referral center. PATIENTS Infants admitted to the neonatal unit who developed P. aeruginosa colonization or infection. METHODS We undertook whole genome sequencing of P. aeruginosa strains isolated from colonized infants and from the neonatal unit environment. RESULTS Eighteen infants were colonized with P. aeruginosa. Isolates from 12 infants and 7 environmental samples were sequenced. All but one of the clinical isolates clustered in ST253 and no differences were detected between unmapped reads. The environmental isolates revealed a variety of sequence types, indicating a large diverse bioburden within the unit, which was subsequently confirmed via enterobacterial repetitive intergenic consensus-polymerase chain reaction typing of post-outbreak isolates. One environmental isolate, obtained from a sink in the unit, clustered within ST253 and differed from the outbreak strain by 9 single-nucleotide polymorphisms only. This information allowed us to focus infection control activities on this sink. CONCLUSIONS Whole genome sequencing can provide detailed information in a clinically relevant time frame to aid management of outbreaks in critical patient management areas. The superior discriminatory power of this method makes it a powerful tool in infection control.
Collapse
|
82
|
Quick J, Ashton P, Calus S, Chatt C, Gossain S, Hawker J, Nair S, Neal K, Nye K, Peters T, De Pinna E, Robinson E, Struthers K, Webber M, Catto A, Dallman TJ, Hawkey P, Loman NJ. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol 2015; 16:114. [PMID: 26025440 PMCID: PMC4702336 DOI: 10.1186/s13059-015-0677-2] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/14/2015] [Indexed: 12/30/2022] Open
Abstract
Background Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patients with Salmonella are at high risk, and require a rapid response. We initially investigated this outbreak by whole-genome sequencing using a novel rapid protocol on the Illumina MiSeq; we then integrated these data with whole-genome data from surveillance sequencing, thereby placing the outbreak in a national context. Additionally, we investigated the potential of a newly released sequencing technology, the MinION from Oxford Nanopore Technologies, in the management of a hospital outbreak of Salmonella. Results We demonstrate that rapid MiSeq sequencing can reduce the time to answer compared to the standard sequencing protocol with no impact on the results. We show, for the first time, that the MinION can acquire clinically relevant information in real time and within minutes of a DNA library being loaded. MinION sequencing permits confident assignment to species level within 20 min. Using a novel streaming phylogenetic placement method samples can be assigned to a serotype in 40 min and determined to be part of the outbreak in less than 2 h. Conclusions Both approaches yielded reliable and actionable clinical information on the Salmonella outbreak in less than half a day. The rapid availability of such information may facilitate more informed epidemiological investigations and influence infection control practices. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0677-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. .,NIHR Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, Birmingham, B15 2TT, UK.
| | | | - Szymon Calus
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. .,NIHR Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Carole Chatt
- Public Health England, Field Epidemiology Service (Birmingham Office), Birmingham, UK.
| | - Savita Gossain
- Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK.
| | - Jeremy Hawker
- Public Health England, Field Epidemiology Service (Birmingham Office), Birmingham, UK.
| | | | - Keith Neal
- Public Health England, Field Epidemiology Service (Birmingham Office), Birmingham, UK.
| | - Kathy Nye
- Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK.
| | | | | | - Esther Robinson
- Department of Microbiology, University of Warwick, Warwick, UK.
| | - Keith Struthers
- Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK.
| | - Mark Webber
- NIHR Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Andrew Catto
- Medical Directorate, Heart of England NHS Trust, Birmingham, UK.
| | | | - Peter Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. .,Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK.
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.
| |
Collapse
|
83
|
Affiliation(s)
- Susannah J Salter
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| |
Collapse
|