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Chagas ADLD, Araújo JCDS, Serra JCP, de Araújo KM, Cunha MDO, Correia ADR, Gonçalves LMB, Carneiro LC. Co-Infection of SARS-CoV-2 and Klebsiella pneumoniae: A Systematic Review and Meta-Analysis. Diagnostics (Basel) 2024; 14:1149. [PMID: 38893674 PMCID: PMC11171625 DOI: 10.3390/diagnostics14111149] [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: 04/30/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
The study aimed to assess the prevalence of COVID-19 and Klebsiella spp. coinfection across continents. Conducted following PRISMA guidelines, a systematic review utilized PubMed, Embase, SCOPUS, ScienceDirect, and Web of Science databases, searching for literature in English published from December 2019 to December 2022, using specific Health Sciences descriptors. A total of 408 records were identified, but only 50 were eligible, and of these, only 33 were included. Thirty-three references were analyzed to evaluate the correlation between COVID-19 and Klebsiella spp. infections. The tabulated data represented a sample group of 8741 coinfected patients. The findings revealed notable disparities in co-infection rates across continents. In Asia, 23% of individuals were infected with Klebsiella pneumoniae, while in Europe, the proportion of co-infected patients stood at 15%. Strikingly, on the African continent, 43% were found to be infected with Klebsiella pneumoniae, highlighting significant regional variations. Overall, the proportion of Klebsiella pneumoniae co-infections among COVID-positive individuals were determined to be 19%. Particularly concerning was the observation that 1 in 6 ICU coinfections was attributed to Klebsiella pneumoniae, indicating its substantial impact on patient outcomes and healthcare burden. The study underscores the alarming prevalence of co-infection between COVID-19 and Klebsiella pneumoniae, potentially exacerbating the clinical severity of patients and posing challenges to treatment strategies. These findings emphasize the importance of vigilant surveillance and targeted interventions to mitigate the adverse effects of bacterial coinfections in the context of the COVID-19 pandemic.
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Affiliation(s)
- Angelica de Lima das Chagas
- Health Science Post Graduation, Federal University of Goias, Goiania 74605-050, Goias, Brazil; (A.d.L.d.C.); (J.C.P.S.); (K.M.d.A.); (M.d.O.C.); (A.d.R.C.)
| | | | - Jaqueline Correia Pontes Serra
- Health Science Post Graduation, Federal University of Goias, Goiania 74605-050, Goias, Brazil; (A.d.L.d.C.); (J.C.P.S.); (K.M.d.A.); (M.d.O.C.); (A.d.R.C.)
| | - Kelliane Martins de Araújo
- Health Science Post Graduation, Federal University of Goias, Goiania 74605-050, Goias, Brazil; (A.d.L.d.C.); (J.C.P.S.); (K.M.d.A.); (M.d.O.C.); (A.d.R.C.)
| | - Marcos de Oliveira Cunha
- Health Science Post Graduation, Federal University of Goias, Goiania 74605-050, Goias, Brazil; (A.d.L.d.C.); (J.C.P.S.); (K.M.d.A.); (M.d.O.C.); (A.d.R.C.)
| | - Amanda dos Reis Correia
- Health Science Post Graduation, Federal University of Goias, Goiania 74605-050, Goias, Brazil; (A.d.L.d.C.); (J.C.P.S.); (K.M.d.A.); (M.d.O.C.); (A.d.R.C.)
| | - Laura Maria Barbosa Gonçalves
- Postgraduate Program in Biology of Host Parasite Relationship, Federal University of Goias, Goiania 74690-900, Goias, Brazil;
| | - Lilian Carla Carneiro
- Health Science Post Graduation, Federal University of Goias, Goiania 74605-050, Goias, Brazil; (A.d.L.d.C.); (J.C.P.S.); (K.M.d.A.); (M.d.O.C.); (A.d.R.C.)
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Almehdar H, Yousef N, van den Boogaard W, Haider A, Kanapathipillai R, Al-Hodiani E, Zelikova E, Moh’d WG, Michel J, Malaeb R. Antibiotic susceptibility patterns at the Médecins Sans Frontières (MSF) Acute Trauma Hospital in Aden, Yemen: a retrospective study from January 2018 to June 2021. JAC Antimicrob Resist 2024; 6:dlae024. [PMID: 38449518 PMCID: PMC10914454 DOI: 10.1093/jacamr/dlae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 02/02/2024] [Indexed: 03/08/2024] Open
Abstract
Background Antimicrobial resistance (AMR) is an urgent global health concern, especially in countries facing instability or conflicts, with compromised healthcare systems. Médecins Sans Frontières (MSF) established an acute trauma hospital in Aden, Yemen, treating mainly war-wounded civilians, and implemented an antimicrobial stewardship (AMS) programme. This study aimed to describe clinical characteristics and identify antibiotic susceptibility patterns representative of patients treated with antibiotics. Methods Retrospective cross-sectional study using routinely collected data from all patients treated with antibiotics in the MSF-Aden Acute Trauma hospital between January 2018 and June 2021. Routine clinical data from patients' files was entered into an AMS electronic database and microbiological data were entered into WHONET. Both databases were imported and merged in REDCap and analysed using RStudio. Results Three hundred and sixty-three of 481 (75%) included patients were injured by violence-related trauma. Most were men aged 19-45 years (n = 331; 68.8%). In total, 598 infections were diagnosed and treated. MDR organisms were identified in 362 (60.5%) infections in 311 (65%) patients. Skin and soft-tissue infections (SSTIs) (n = 143; 24%) were the most common, followed by osteomyelitis (n = 125; 21%) and intra-abdominal-infections (IAIs) (n = 116; 19%), and 111 (19%) secondary bloodstream infections were identified. Escherichia coli was the most frequently identified pathogen, causing IAI (n = 87; 28%) and SSTI (n = 43; 16%), while Staphylococcus aureus caused mainly osteomyelitis (n = 84; 19%). Most Gram-negatives were ESBL producers, including E. coli (n = 193; 81.4%), Klebsiella pneumoniae (n = 72; 77.4%) and Enterobacter cloacae (n = 39; 50%) while most S. aureus were methicillin resistant (n = 93; 72.6%). Conclusions High rates of MDR were found. This information will facilitate a comprehensive review of the empirical antibiotic treatment guidelines.
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Affiliation(s)
- Hussein Almehdar
- Médecins Sans Frontières—Operational Centre Paris (MSFOCP), Acute Trauma Hospital, Aden, Yemen
| | - Nagwan Yousef
- Médecins Sans Frontières—Operational Centre Paris (MSFOCP), Acute Trauma Hospital, Aden, Yemen
| | - Wilma van den Boogaard
- Médecins Sans Frontières—Operational Centre Brussels, Medical Department, Luxembourg Operational Research (LuxOR) Unit, Luxembourg City, Luxembourg
| | - Amna Haider
- Department of Epidemiology and Training, Epicentre, Dubai, United Arab Emirates
| | - Rupa Kanapathipillai
- Médecins Sans Frontières—Operational Centre Paris, Medical Department, Paris, France
| | - Emad Al-Hodiani
- Médecins Sans Frontières—Operational Centre Paris (MSFOCP), Acute Trauma Hospital, Aden, Yemen
| | - Evgenia Zelikova
- Médecins Sans Frontières—Operational Centre Paris, Medical Department, Paris, France
| | - Waddah G Moh’d
- Médecins Sans Frontières—Operational Centre Paris (MSFOCP), Acute Trauma Hospital, Aden, Yemen
| | - Justine Michel
- Médecins Sans Frontières—Operational Centre Paris, Medical Department, Paris, France
| | - Rami Malaeb
- Department of Epidemiology and Training, Epicentre, Dubai, United Arab Emirates
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Álvarez-Ainza ML, Fong-Coronado PA, Ruiz-Bustos E, Castillón-Campaña LG, Quintero-Reyes IE, Duarte-Zambrano LA, Bolado-Martínez E. Antibiotic resistance of ESKAPE group-microorganisms in health institutions from Hermosillo and Ciudad Obregón, Sonora, México. Front Cell Infect Microbiol 2024; 14:1348093. [PMID: 38516533 PMCID: PMC10955632 DOI: 10.3389/fcimb.2024.1348093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
Introduction Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. are microorganisms referred as the ESKAPE group pathogens. These microorganisms have generated great concern in health institutions around the world since most of them have resistance to multiple antibiotics and cause most infections associated with healthcare, as well as community infections. The aim of this study was the analysis of antibiotic resistance in microorganisms of the ESKAPE group, recovered from clinical samples in 11 health institutions from Hermosillo and Ciudad Obregón in the State of Sonora, México, during the period from 2019 to 2020. Methods A cross-sectional, descriptive, observational, and temporality epidemiological study was carried out. A comparative and statistical analysis of antibiotic resistance was carried out using the chi-square test, and small values were analyzed using Fisher's exact test p ≤ 0.05. Results and discussion All the ESKAPE group microorganisms showed significant differences in antibiotic resistance percentages between both cities. High resistance percentages for some antibiotics, like cephalosporins and ciprofloxacin were detected for Klebsiella pneumoniae and Acinetobacter baumannii.
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Affiliation(s)
- Maritza Lizeth Álvarez-Ainza
- Laboratorio de Microbiología, Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Pedro Alejandro Fong-Coronado
- Laboratorio de Microbiología, Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Eduardo Ruiz-Bustos
- Laboratorio de Microbiología, Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | | | - Idania Emedith Quintero-Reyes
- Laboratorio de Análisis Especializantes, Departamento de Ciencias de la Salud, Universidad de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Luis Armando Duarte-Zambrano
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI) Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Enrique Bolado-Martínez
- Laboratorio de Microbiología, Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
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Khound P, Pandya H, Patel R, Patel N, Darji SA, Trivedi P, Mehta V, Raulji A, Banerjee D. An Approach to Track and Analyze the Trend of Antimicrobial Resistance Using Python: A Pilot Study for Anand, Gujarat, India-May 2022-August 2023. Microb Drug Resist 2024; 30:1-20. [PMID: 38150701 DOI: 10.1089/mdr.2023.0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023] Open
Abstract
The present work deals with the analysis and monitoring of bacterial resistance in using Python for the state of Gujarat, India, where occurrences of drug-resistant bacteria are prevalent. This will provide an insight into the portfolio of drug-resistant bacteria reported, which can be used to track resistance behavior and to suggest a treatment regime for the particular bacteria. The present analysis has been done using Python on Jupyter Notebook as the integrated development environment and its data analysis libraries such as Pandas, Seaborn, and Matplotlib. The data have been loaded from excel file using Pandas and cleaned to transform features into required format. Seaborn and Matplotlib have been used to create data visualizations and represent the data inexplicable manner using graphs, plots, and tables. This program can be used to study disaster epidemiology, tracking, analyzing, and surveillance of antimicrobial resistance with a proper system integration approach.
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Affiliation(s)
| | - Himanshu Pandya
- Department of Microbiology, Pramukhswami Medical College, Bhaikaka University, Karamsad Medical College, Anand, Gujarat, India
| | - Rupal Patel
- Department of Microbiology, Pramukhswami Medical College, Bhaikaka University, Karamsad Medical College, Anand, Gujarat, India
| | - Naimika Patel
- Department of Microbiology, Pramukhswami Medical College, Bhaikaka University, Karamsad Medical College, Anand, Gujarat, India
| | - Siddhi A Darji
- School of Sciences, GSFC University, Vadodara, Gujarat, India
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology Department, The M S University of Baroda, Vadodara, Gujarat, India
| | - Purvi Trivedi
- School of Sciences, GSFC University, Vadodara, Gujarat, India
| | - Vandan Mehta
- School of Sciences, GSFC University, Vadodara, Gujarat, India
| | - Avani Raulji
- Department of Microbiology, Pramukhswami Medical College, Bhaikaka University, Karamsad Medical College, Anand, Gujarat, India
| | - Devjani Banerjee
- School of Sciences, GSFC University, Vadodara, Gujarat, India
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology Department, The M S University of Baroda, Vadodara, Gujarat, India
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Aboushady AT, Sujan MJ, Pham K, Clark A, Marks F, Holm M, Joh HS, Poudyal N, Stelling J. Key Recommendations for Antimicrobial Resistance Surveillance: Takeaways From the CAPTURA Project. Clin Infect Dis 2023; 77:S581-S587. [PMID: 38118016 PMCID: PMC10732552 DOI: 10.1093/cid/ciad487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023] Open
Abstract
Antimicrobial resistance (AMR) is a growing global public health challenge associated with 4.95 million deaths in 2019 and an estimated 10 million deaths per year by 2050 in the absence of coordinated action. A robust AMR surveillance system is therefore required to avert such a scenario. Based on an analysis of country-level AMR data in 8 Capturing Data on Antimicrobial Resistance Patterns and Trends in Use in Regions of Asia (CAPTURA) countries, we present a list of key recommendations to strengthen AMR surveillance. We propose 10 primary considerations under 3 broad categories, including recommendations on (1) laboratory and testing practices, (2) data management and analysis, and (3) data use.
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Affiliation(s)
- Ahmed Taha Aboushady
- Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- International Vaccine Institute, Seoul, Republic of Korea
| | | | - Kien Pham
- International Vaccine Institute, Seoul, Republic of Korea
| | - Adam Clark
- Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Marianne Holm
- International Vaccine Institute, Seoul, Republic of Korea
| | - Hea Sun Joh
- International Vaccine Institute, Seoul, Republic of Korea
| | - Nimesh Poudyal
- International Vaccine Institute, Seoul, Republic of Korea
| | - John Stelling
- Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Zafeiridis C, Valiakos G, Giakoupi P, Papadogiannakis E. Building the National Antimicrobial Resistance Surveillance Network in Animals in Greece: A "One Health" Approach. Antibiotics (Basel) 2023; 12:1442. [PMID: 37760738 PMCID: PMC10525538 DOI: 10.3390/antibiotics12091442] [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: 07/12/2023] [Revised: 08/14/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
It is widely accepted that, in order to prevent and control antimicrobial resistance (AMR), surveillance systems across human, animal and environmental sectors need to be integrated, in a One Health approach. Currently, in Europe, there are surveillance networks established only for the human and food sector and, until now, there has been no organized effort to monitor AMR in bacterial pathogens derived from diseased animals in Europe. Since 2017, efforts to fill this gap have taken place by the European Antimicrobial Resistance Surveillance network in a veterinary medicine (EARS-Vet) initiative, included in the EU Joint Action on AMR and Healthcare-Associated Infections (EU-JAMRAI). EARS-Vet is designed to complement and integrate with existing European monitoring systems for AMR as well as constitute a European network of national monitoring systems. As Greece has no national AMR surveillance system for pathogens of animal origin currently in place, in the context of the development of EARS-Vet, an initiative took place for the organization of such a system by competent agencies and other stakeholders. In this article, the steps to organize a first AMR national surveillance network in Greece are presented and a Strengths, Weaknesses, Opportunities, and Threats (SWOT) analysis is performed to present main characteristics of the approach implemented.
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Affiliation(s)
- Christos Zafeiridis
- General Directorate of Veterinary Services, Ministry of Rural Development & Food of Greece, 10176 Athens, Greece;
| | - George Valiakos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece;
| | - Panagiota Giakoupi
- Department of Public Health Policy, School of Public Health, University of West Attica, 11521 Athens, Greece;
| | - Emmanouil Papadogiannakis
- Department of Public Health Policy, School of Public Health, University of West Attica, 11521 Athens, Greece;
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Hill DM, Todor LA. Deficiencies of Rule-Based Technology-Generated Antibiograms for Specialized Care Units. Antibiotics (Basel) 2023; 12:1002. [PMID: 37370321 DOI: 10.3390/antibiotics12061002] [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: 04/29/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
The objective of this study was to compare the pathogens and susceptibilities of the current automated, rule-based technology (RBT) antibiogram with one manually collected through chart review with additional rules applied. This study was a two-year, retrospective cohort study and included all bacterial cultures within the first 30 days from patients admitted to a single Burn Center. The current RBT antibiogram served as the control, and new antibiogram versions were created using additional rules and compared to the control. Six-hundred fifty-seven patients were admitted (61% excluded for lack of cultures). 59% had at least one hospital-acquired risk factor, with over one-third having recent illicit drug use and one-third having a recent hospitalization. Of the 410 cultures included, 57% were Gram-negative, and half were from wound infections. Sensitivities were significantly different when comparing the manual and the RBT version after including factors such as days since admission, presence of hospital-acquired risk factors, or previous antibiotic courses. Recommended empiric Gram-negative antibiotics changed from double coverage to a single β-lactam with >90% susceptibility. The susceptibilities between the first and subsequent courses were dramatically different. Before developing an antibiogram or interpreting the output, it is important to consider which automated criteria are utilized, especially for units with extended lengths of stay.
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Affiliation(s)
- David M Hill
- Department of Pharmacy, Regional One Health, Memphis, TN 38103, USA
| | - Lorraine A Todor
- Department of Pharmacy, Regional One Health, Memphis, TN 38103, USA
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High prevalence of antimicrobial resistance and multidrug resistance among bacterial isolates from diseased pets: Retrospective laboratory data (2015-2017). PLoS One 2022; 17:e0277664. [PMID: 36477195 PMCID: PMC9728933 DOI: 10.1371/journal.pone.0277664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
Laboratory surveillance and the monitoring of antimicrobial resistance (AMR) trends and patterns among local isolates have been highly effective in providing comprehensive information for public health decision-making. A total of 396 cases along with 449 specimens were received for antibiotic susceptibility testing at a public university veterinary diagnostic laboratory in Malaysia between 2015 and 2017. Escherichia coli was the most frequently isolated (n = 101, 13%) bacteria, followed by Staphylococcus pseudintermedius (n = 97, 12%) and Streptococcus canis (n = 62, 8%). In cats, S. pseudintermedius isolates were highly resistant to azithromycin (90%), while the E. coli isolates were highly resistant to doxycycline (90%), tetracycline (81%), and cephalexin (75%). About 55% of S. pseudintermedius and 82% of E. coli were multi-drug resistant (MDR). In dogs, S. intermedius isolates were highly resistant to aminoglycosides neomycin (90.9%) and gentamicin (84.6%), and tetracycline (75%). Whereas the E. coli isolates were highly resistant to cephalexin (82.1%) and amoxicillin/clavulanic acid (76.5%). MDR was observed in 60% of S. intermedius and 72% of E. coli from dogs. Generally, the bacterial isolates from cats demonstrated higher levels of resistance to multiple antibiotics compared to those from dogs.
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Yaacoub S, Truppa C, Pedersen TI, Abdo H, Rossi R. Antibiotic resistance among bacteria isolated from war-wounded patients at the Weapon Traumatology Training Center of the International Committee of the Red Cross from 2016 to 2019: a secondary analysis of WHONET surveillance data. BMC Infect Dis 2022; 22:257. [PMID: 35287597 PMCID: PMC8922823 DOI: 10.1186/s12879-022-07253-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background A substantial body of evidence has recently emphasized the risks associated with antibiotic resistance (ABR) in conflicts in the Middle East. War-related, and more specifically weapon-related wounds can be an important breeding ground for multidrug resistant (MDR) organisms. However, the majority of available evidence comes from the military literature focused on risks and patterns of ABR in infections from combat-related injuries among military personnel. The overall aim of this study is to contribute to the scarce existing evidence on the burden of ABR among patients, including civilians with war-related wounds in the Middle East, in order to help inform the revision of empirical antibiotic prophylaxis and treatment protocols adopted in these settings. The primary objectives of this study are to: 1) describe the microbiology and the corresponding resistance profiles of the clinically relevant bacteria most commonly isolated from skin, soft tissue and bone biopsies in patients admitted to the WTTC; and 2) describe the association of the identified bacteria and corresponding resistance profiles with sociodemographic and specimen characteristics. Methods We retrospectively evaluated the antibiograms of all consecutive, non-duplicate isolates from samples taken from patients admitted to the ICRC WTTC between 2016 and 2019, limited to skin and soft tissue samples and bone biopsies. We collected data on socio-demographic characteristics from patient files and data on specimens from the WHONET database. We ran univariate and multivariable logistic regression models to test the association between bacterial and resistance profiles with sociodemographic and specimen characteristics. Results Patients who were admitted with war-related trauma to the ICRC reconstructive surgical project in Tripoli, Lebanon, from 2016 to 2019, presented with high proportion of MDR in the samples taken from skin and soft tissues and bones, particularly Enterobacterales (44.6%), MRSA (44.6%) and P. aeruginosa (7.6%). The multivariable analysis shows that the odds of MDR isolates were higher in Iraqi patients (compared to Syrian patients) and in Enterobacterales isolates (compared to S. aureus isolates). Conclusions Our findings stress the importance of regularly screening patients who present with complex war-related injuries for colonization with MDR bacteria, and of ensuring an antibiotic-sensitivity testing-guided antimicrobial therapeutic approach. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07253-1.
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Affiliation(s)
- Sally Yaacoub
- International Committee of the Red Cross (ICRC), Geneva, Switzerland. .,International Committee of the Red Cross (ICRC), Beirut, Lebanon.
| | - Claudia Truppa
- International Committee of the Red Cross (ICRC), Beirut, Lebanon
| | | | | | - Rodolfo Rossi
- International Committee of the Red Cross (ICRC), Geneva, Switzerland
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Chaplain D, Asutaku BB, Mona M, Bulafu D, Aruhomukama D. The need to improve antimicrobial susceptibility testing capacity in Ugandan health facilities: insights from a surveillance primer. Antimicrob Resist Infect Control 2022; 11:23. [PMID: 35115045 PMCID: PMC8812180 DOI: 10.1186/s13756-022-01072-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/23/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Lab-based surveillance (LBS) of antimicrobial resistance (AMR) is not systematically implemented in Uganda. We aimed to identify the gaps in establishing regular LBS of AMR in Uganda. METHODS This was a retrospective records review. It was done at Mulago Hospital (MH) Microbiology Lab (MHL). It analyzed lab records on bacteria and their antimicrobial susceptibility profiles (ASPs) over 6 months. Since MH is the national referral hospital, we hypothesized that (1) MHL is the best resourced and that any limitations seen here are amplified in labs at regional referral hospitals (RRHs) and health centers (HCs); (2) data from MHL on LBS mirrors that from labs at RRHs and HCs; (3) the state of records from MHL show lab performance and the presence or absence of standard operating procedures (SOPs), as would be the case at RRHs and HCs. RESULTS The lab got 1760 samples over the six months. The most common sample was urine (659, 37.4%). From the 1760 samples, data on 478 bacterial isolates were available. Urine gave the most isolates (159, 33.3%). Most of the isolates were gram-negative (267, 55.9%). Escherichia coli (100, 37%) was the most common gram-negative (of the Enterobacteriaceae). Pseudomonas aeruginosa (17, 6%) was the most common gram-negative (of the non-Enterobacteriaceae). The gram-negative bacteria were highly resistant to β-lactams. These were highly sensitive to carbapenems. The Staphylococcus aureus were highly resistant to β-lactams. The gram-positive bacteria were highly sensitive to vancomycin. ASPs for all bacterial categories were incomplete. CONCLUSIONS The findings from MHL suggest that there is a need to improve antimicrobial susceptibility testing capacity. They also suggest that the situation at RRHs and HCs around the country could be worse. So, there is a need to extend the political will, which already exists, into operational and implementation action.
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Affiliation(s)
- Duku Chaplain
- Clinical Microbiology Laboratory, Mulago National Referral Hospital, Kampala, Uganda
| | - Butti Ben Asutaku
- Clinical Microbiology Laboratory, Mulago National Referral Hospital, Kampala, Uganda
| | - Muhammad Mona
- Clinical Microbiology Laboratory, Mulago National Referral Hospital, Kampala, Uganda
| | - Douglas Bulafu
- Department of Disease Control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Dickson Aruhomukama
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
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Krishnamoorthy SG, Raj V, Viswanathan B, Dhanasekaran GP, Palaniappan D, Borra SS. Enhancing the empiric antibiotic selection by introducing an antibiogram toolkit in a tertiary care hospital in Southern India - A prospective study. J Clin Pharm Ther 2021; 47:507-516. [PMID: 34962298 DOI: 10.1111/jcpt.13571] [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: 10/06/2021] [Revised: 10/24/2021] [Accepted: 11/01/2021] [Indexed: 11/30/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE Antibiograms gives an overview of the cumulative susceptibility of formal antibiotics to bacterial isolates, which reflects the portion of each bacterium susceptible to a given antibiotic formulation by using antimicrobial susceptibility testing. The objective of this study is to gather and analyse data from drug utilization evaluation (DUE) studies and antimicrobial susceptibility tests in order to create an antibiogram toolkit that will help clinicians to select appropriate antimicrobial agents for initial empirical antibiotic therapy at point of care settings and avoid irrational use of antibiotics. METHODS A prospective interventional study was conducted at tertiary care hospital, biological samples of infectious patients were collected from various wards as per Clinical & Laboratory Standards Institute CLSI M39-A4 guidelines. Antimicrobial susceptibility results were analysed using WHONET software. Antibiotic stewardship committee was formed and involved in monitoring the usage of antibiotics, measuring outcomes, collecting feedback and finding the scope for improving the application of antibiogram toolkit in the hospital. Antibiotic usage tracking method was followed to know the level of adherence to the prescribing guidelines by the health care professionals. RESULTS AND DISCUSSION A total of 157 samples were obtained from various wards of the hospital. In that, Escherichia coli, Staphylococcus aureus and Klebsiella Pneumoniae were isolated in significant numbers. Antibacterial susceptibility results were collected, an initial antibiogram was developed for 18 antibacterial agents with respect to 3 gram-positive (+) and 1 gram-negative (-) organisms. 90% of prescribers mentioned that the antibiogram was useful, and 76% of them adhered to the guidelines. 26% were not adhered due to the patient-related factors. WHAT IS NEW AND CONCLUSION In our study, we have used qualitative and quantitative evaluation of drug utilization (DUE) reports to understand the existing prescribing pattern of antibiotics and setting target organisms and antibacterials to develop the hospital antibiogram. Combining DUE studies and antibiogram development was helpful in implementing effective antibiotic policies for the hospital. Further, this study pattern will be continued on a yearly basis and focused on developing cumulative antibiograms to understand the changes in resistance pattern of antimicrobials and utilization of antibiotics in the hospital.
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Affiliation(s)
- Sadagoban G Krishnamoorthy
- Department of Pharmacy Practice, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
| | - Vyshak Raj
- Department of Pharmacy Practice, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
| | | | - Ganga Priyadharshini Dhanasekaran
- Department of Pharmacy Practice, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
| | - Dhivyaprasath Palaniappan
- Department of Pharmacy Practice, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
| | - Swathi Swaroopa Borra
- Department of Pharmacy Practice, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
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12
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Ali S, Dennehy F, Donoghue O, McNicholas S. Antimicrobial susceptibility patterns of anaerobic bacteria at an Irish University Hospital over a ten-year period (2010-2020). Anaerobe 2021; 73:102497. [PMID: 34875368 DOI: 10.1016/j.anaerobe.2021.102497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 11/18/2022]
Abstract
OBJECTIVES In recent years various clinical studies have demonstrated poor outcomes in infections caused by anaerobic bacteria due to inappropriate therapy, directly due to emergence of resistant strains. This is a concern given that many anaerobic infections are treated empirically with metronidazole or a beta-lactam/beta-lactamase inhibitor combinations (e.g., co-amoxiclav, piperacillin-tazobactam). To date there is a paucity of available data on antimicrobial resistance trends of anaerobic bacteria in Ireland, and our study aims to determine such patterns among isolates processed at our institution over the last ten years. METHODS Significant anaerobic bacteria isolated from clinical specimens processed at our laboratory from January 2010 to January 2020 inclusive were reviewed. Bacteria were identified using MALDI-TOF, with E-tests used for antimicrobial susceptibility testing. Data was processed through WHONET. RESULTS A total of 2098 clinically significant anaerobic bacterial isolates from blood cultures (31%), theatre/intraoperative specimens (30%), aspirates and drain fluid (22%) and wound swabs (17%) were reviewed during the study period; with the majority of isolates being Bacteroides spp (32.79%, n = 688) and Clostridium spp (18.68%, n = 392). With isolates demonstrating well-recognised or inherent resistances excluded, overall resistance to tested antimicrobials was 6.40% to penicillin, 1.71% to metronidazole, 1.43% to co-amoxiclav, 13.63% to clindamycin, 0.43% to piperacillin-tazobactam and 0% to meropenem. CONCLUSION Metronidazole and beta-lactam/beta-lactamase inhibitor combinations remain highly efficacious against the majority of anaerobic isolates reviewed, and can safely be used as empiric therapy in suspected anaerobic infections. However, periodic surveillance of resistance trends remains important.
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Affiliation(s)
- Saied Ali
- Department of Microbiology, St Vincent's University Hospital, Elm Park, Dublin, D04 T6F4, Ireland.
| | - Frank Dennehy
- Department of Microbiology, St Vincent's University Hospital, Elm Park, Dublin, D04 T6F4, Ireland.
| | - Orla Donoghue
- Department of Microbiology, St Vincent's University Hospital, Elm Park, Dublin, D04 T6F4, Ireland.
| | - Sinead McNicholas
- Department of Microbiology, St Vincent's University Hospital, Elm Park, Dublin, D04 T6F4, Ireland.
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Kaur J, Kaur J, Kapoor S, Singh H. Design & development of customizable web API for interoperability of antimicrobial resistance data. Sci Rep 2021; 11:11226. [PMID: 34045584 PMCID: PMC8160260 DOI: 10.1038/s41598-021-90601-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global health emergency. Complementary to developing new drugs, AMR can be monitored and controlled through cost-effective active surveillance of resistance. As an initiative to monitor resistance, countries all across the globe are collecting data using a variety of surveillance tools. Moreover, hospitals routinely collect the AMR data for treatment which is being stored in their Laboratory and Hospital Information systems (LIS-HIS). The generated clinical data is collected & stored in various formats, making it very difficult to analyze and generate national reports. To integrate the stored clinical data for predictive modeling and analysis, there is an immediate need for a one-stop data repository capable of importing and exporting data in simple data exchange formats (CSV/Excel). The paper highlights the design & development of i-DIA, a python-based web API to facilitate the interoperability of AMR data by automatically importing the bulk of medical data from CSV files into generic data management and analysis system. The i-DIA has been integrated and tested with the ICMR's AMR surveillance network on in-house developed software, i-AMRSS. The i-AMRSS is presently collecting data from 31 laboratories across India and i-DIA has been used to import data generated from LIS & HIS of a few hospitals directly into the system. The paper also proposes the complete web-based framework (an extension of i-DIA) integrated with peer-to-peer system architecture.
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Affiliation(s)
- Jasleen Kaur
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, 110029, India
| | - Jasmine Kaur
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, 110029, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
- Data Science Laboratory, Amity Institute of Integrative Science & Health, Amity University Gurgaon, Gurgaon, India
| | - Shruti Kapoor
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, 110029, India
| | - Harpreet Singh
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, 110029, India.
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Haulisah NA, Hassan L, Bejo SK, Jajere SM, Ahmad NI. High Levels of Antibiotic Resistance in Isolates From Diseased Livestock. Front Vet Sci 2021; 8:652351. [PMID: 33869326 PMCID: PMC8047425 DOI: 10.3389/fvets.2021.652351] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/09/2021] [Indexed: 12/20/2022] Open
Abstract
Overuse of antimicrobials in livestock health and production beyond therapeutic needs has been highlighted in recent years as one of the major risk factors for the acceleration of antimicrobial resistance (AMR) of bacteria in both humans and animals. While there is an abundance of reports on AMR in clinical isolates from humans, information regarding the patterns of resistance in clinical isolates from animals is scarce. Hence, a situational analysis of AMR based on clinical isolates from a veterinary diagnostic laboratory was performed to examine the extent and patterns of resistance demonstrated by isolates from diseased food animals. Between 2015 and 2017, 241 cases of diseased livestock were received. Clinical specimens from ruminants (cattle, goats and sheep), and non-ruminants (pigs and chicken) were received for culture and sensitivity testing. A total of 701 isolates were recovered from these specimens. From ruminants, Escherichia coli (n = 77, 19.3%) predominated, followed by Staphylococcus aureus (n = 73, 18.3%). Antibiotic sensitivity testing (AST) revealed that E. coli resistance was highest for penicillin, streptomycin, and neomycin (77-93%). In addition, S. aureus was highly resistant to neomycin, followed by streptomycin and ampicillin (68-82%). More than 67% of E. coli isolates were multi-drug resistant (MDR) and only 2.6% were susceptible to all the tested antibiotics. Similarly, 65.6% of S. aureus isolates were MDR and only 5.5% were susceptible to all tested antibiotics. From non-ruminants, a total of 301 isolates were recovered. Escherichia coli (n = 108, 35.9%) and Staphylococcus spp. (n = 27, 9%) were the most frequent isolates obtained. For E. coli, the highest resistance was against amoxicillin, erythromycin, tetracycline, and neomycin (95-100%). Staphylococcus spp. had a high level of resistance to streptomycin, trimethoprim/sulfamethoxazole, tetracycline and gentamicin (80-100%). The MDR levels of E. coli and Staphylococcus spp. isolates from non-ruminants were 72.2 and 74.1%, respectively. Significantly higher resistance level were observed among isolates from non-ruminants compared to ruminants for tetracycline, amoxicillin, enrofloxacin, and trimethoprim/sulfamethoxazole.
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Affiliation(s)
| | - Latiffah Hassan
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Siti Khairani Bejo
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | | | - Nur Indah Ahmad
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
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15
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Park CE. Evaluation of the Effectiveness of Surveillance on Improving the Detection of Healthcare Associated Infections. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2019. [DOI: 10.15324/kjcls.2019.51.1.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Chang-Eun Park
- Department of Biomedical Laboratory Science, Molecular Diagnostics Research Institute, Namseoul University, Cheonan, Korea
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16
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Ershova K, Savin I, Kurdyumova N, Wong D, Danilov G, Shifrin M, Alexandrova I, Sokolova E, Fursova N, Zelman V, Ershova O. Implementing an infection control and prevention program decreases the incidence of healthcare-associated infections and antibiotic resistance in a Russian neuro-ICU. Antimicrob Resist Infect Control 2018; 7:94. [PMID: 30083313 PMCID: PMC6069828 DOI: 10.1186/s13756-018-0383-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/18/2018] [Indexed: 11/10/2022] Open
Abstract
Background The impact of infection prevention and control (IPC) programs in limited resource countries such as Russia are largely unknown due to a lack of reliable data. The aim of this study is to evaluate the effect of an IPC program with respect to healthcare associated infection (HAI) prevention and to define the incidence of HAIs in a Russian ICU. Methods A pioneering IPC program was implemented in a neuro-ICU at Burdenko Neurosurgery Institute in 2010 and included hand hygiene, surveillance, contact precautions, patient isolation, and environmental cleaning measures. This prospective observational cohort study lasted from 2011 to 2016, included high-risk ICU patients, and evaluated the dynamics of incidence, etiological spectrum, and resistance profile of four types of HAIs, including subgroup analysis of device-associated infections. Survival analysis compared patients with and without HAIs. Results We included 2038 high-risk patients. By 2016, HAI cumulative incidence decreased significantly for respiratory HAIs (36.1% vs. 24.5%, p-value = 0.0003), urinary-tract HAIs (29.1% vs. 21.3%, p-value = 0.0006), and healthcare-associated ventriculitis and meningitis (HAVM) (16% vs. 7.8%, p-value = 0.004). The incidence rate of EVD-related HAVM dropped from 22.2 to 13.5 cases per 1000 EVD-days. The proportion of invasive isolates of Klebsiella pneumoniae and Acinetobacter baumannii resistant to carbapenems decreased 1.7 and 2 fold, respectively. HAVM significantly impaired survival and independently increasing the probability of death by 1.43. Conclusions The implementation of an evidence-based IPC program in a middle-income country (Russia) was highly effective in HAI prevention with meaningful reductions in antibiotic resistance. Electronic supplementary material The online version of this article (10.1186/s13756-018-0383-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ksenia Ershova
- 1Center for Data-Intensive Biotechnology and Biomedicine, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ivan Savin
- Department of Intensive Care, Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - Nataliya Kurdyumova
- Department of Intensive Care, Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - Darren Wong
- 3Division of Infectious Diseases, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Gleb Danilov
- Laboratory of Biomedical Informatics, Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - Michael Shifrin
- IT Department, Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - Irina Alexandrova
- Department of Microbiology, Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - Ekaterina Sokolova
- Department of Intensive Care, Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - Nadezhda Fursova
- Federal Budget Institution of Science "State Research Center for Applied Microbiology & Biotechnology" (SRCAMB), Moscow, Russia
| | - Vladimir Zelman
- 1Center for Data-Intensive Biotechnology and Biomedicine, Skolkovo Institute of Science and Technology, Moscow, Russia.,8Department of Anesthesiology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Olga Ershova
- Department of Epidemiology and Infection Control, Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
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Kalule JB, Fortuin S, Calder B, Robberts L, Keddy KH, Nel AJM, Garnett S, Nicol M, Warner DF, Soares NC, Blackburn JM. Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagar™STEC media. J Proteomics 2017; 180:25-35. [PMID: 28887208 DOI: 10.1016/j.jprot.2017.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 08/21/2017] [Accepted: 09/02/2017] [Indexed: 02/06/2023]
Abstract
Shiga-toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) are key diarrhoea-causing foodborne pathogens. We used proteomics to characterize the virulence and antimicrobial resistance protein profiles of three clinical pathogenic E. coli isolates (two EPEC [one resistant to ciprofloxacin] and one STEC) cultured on CHROMagar™STEC solid media after minimal laboratory passage. We identified 4767 unique peptides from 1630 protein group across all three clinical E. coli strains. Label-free proteomic analysis allowed the identification of virulence and drug resistance proteins that were unique to each of the clinical isolates compared in this study. The B subunit of Shiga toxin, ToxB, was uniquely detected in the STEC strain while several other virulence factors including SheA, OmpF, OmpC and OmpX were significantly more abundant in the STEC strain. The ciprofloxacin resistant EPEC isolate possessed reduced levels of key virulence proteins compared to the ciprofloxacin susceptible EPEC and STEC strains. Parallel reaction monitoring assays validated the presence of biologically relevant proteins across biologically-replicated cultures. Propagation of clinical isolates on a relevant solid medium followed by mass spectrometry analysis represents a convenient means to quantify virulence factors and drug resistance determinants that might otherwise be lost through extensive in vitro passage in enteropathogenic bacteria. SIGNIFICANCE Through the use of quantitative proteomics, we have characterized the virulence and antimicrobial resistance attributes of three clinically isolated, pathogenic E. coli strains cultured on solid media. Our results provide new, quantitative data on the expressed proteomes of these tellurite-resistant, diarrhoeagenic E. coli strains and reveal a subset of antimicrobial resistance and virulence proteins that are differentially abundant between these clinical strains. Our quantitative proteomics-based approach should thus have applicability in microbiological diagnostic labs for the identification of pathogenic/drug resistant E. coli in the future.
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Affiliation(s)
- John Bosco Kalule
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Suereta Fortuin
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Bridget Calder
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Lourens Robberts
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Karen H Keddy
- Bacteriology Division, Centre for Enteric Diseases, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew J M Nel
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Shaun Garnett
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark Nicol
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa
| | - Digby F Warner
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa; MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Medical Microbiology, Department of Pathology, University of Cape Town, South Africa
| | - Nelson C Soares
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa.
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Liang W, Xie Y, Xiong W, Tang Y, Li G, Jiang X, Lu Y. Anti-Restriction Protein, KlcA HS, Promotes Dissemination of Carbapenem Resistance. Front Cell Infect Microbiol 2017; 7:150. [PMID: 28512626 PMCID: PMC5411435 DOI: 10.3389/fcimb.2017.00150] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/11/2017] [Indexed: 11/13/2022] Open
Abstract
Carbapenemase-producing Klebsiella pneumoniae (KPC) has emerged and spread throughout the world. A retrospective analysis was performed on carbapenem-resistant K. pneumoniae isolated at our teaching hospital during the period 2009–2010, when the initial outbreak occurred. To determine the mechanism(s) that underlies the increased infectivity exhibited by KPC, Multilocus Sequence Typing (MLST) was conducted. A series of plasmids was also extracted, sequenced and analyzed. Concurrently, the complete sequences of blaKPC−2-harboring plasmids deposited in GenBank were summarized and aligned. The blaKPC−2 and KlcAHS genes in the carbapenem-resistant K. pneumoniae isolates were examined. E. coli strains, carrying different Type I Restriction and Modification (RM) systems, were selected to study the interaction between RM systems, anti-RM systems and horizontal gene transfer (HGT). The ST11 clone predominated among 102 carbapenem-resistant K. pneumoniae isolates, all harbored the blaKPC−2 gene; 98% contained the KlcAHS gene. KlcAHS was one of the core genes in the backbone region of most blaKPC−2 carrying plasmids. Type I RM systems in the host bacteria reduced the rate of pHS10842 plasmid transformation by 30- to 40-fold. Presence of the anti-restriction protein, KlcAHS, on the other hand, increased transformation efficiency by 3- to 6-fold. These results indicate that RM systems can significantly restrict HGT. In contrast, KlcAHS can disrupt the RM systems and promote HGT by transformation. These findings suggest that the anti-restriction protein, KlcAHS, represents a novel mechanism that facilitates the increased transfer of blaKPC-2 and KlcAHS-carrying plasmids among K. pneumoniae strains.
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Affiliation(s)
- Wei Liang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan UniversityShanghai, China
| | - Yingzhou Xie
- State Key Laboratory for Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong UniversityShanghai, China
| | - Wei Xiong
- State Key Laboratory for Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong UniversityShanghai, China
| | - Yu Tang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan UniversityShanghai, China
| | - Gang Li
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan UniversityShanghai, China
| | - Xiaofei Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan UniversityShanghai, China
| | - Yuan Lu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan UniversityShanghai, China
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