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Quan Z, Xu J, Li M, Cheng C, Mijiti P, Jiang Q, Takiff H, Ren Z, Gao Q. Transmission of tuberculosis in rural Henan, China: a prospective population-based genomic spatial epidemiological study. Emerg Microbes Infect 2024; 13:2399273. [PMID: 39207222 PMCID: PMC11378662 DOI: 10.1080/22221751.2024.2399273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/21/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
The incidence of tuberculosis (TB) has declined more slowly in rural than urban areas in China, and data on the patterns of transmission and the high-risk populations in rural areas remains scarce. We conducted a population-based study of culture-positive pulmonary TB patients diagnosed in rural Linzhou City, Henan Province from July 2018 to February 2023. Genomic clusters were defined based on whole-genome sequencing and risk factors for clustering were identified by logistic regression. Transmission events were inferred with phybreak and transmission links were sought through epidemiological investigation of clustered patients. Logistic regression was used to explore the relationship between genomic differences of patient isolates and geographical distances of patient residences. Spatial hotspots were defined using kernel density estimation. Of 455 culture-positive patients, 430 were included in the final analysis. Overall, 192 (44.7%,192/430) patients were grouped into 49 clusters. Clusters containing ≥5 patients accounted for 18.4% (9/49) of the clusters and clustering was highest in student patients. No super-spreaders were detected. Confirmed epidemiologic links were identified for only 18.2% of clustered patients. The clustering risk decreased rapidly with increasing distances between patient residences, but 77.6% of clustered patient pairs lived ≥5.0 km apart. Both the Central Subdistrict and Rencun Township were identified as hotspots for TB transmission. Recent transmission appears to be an important driver of the TB burden in Linzhou. The formulation of effective strategies to reduce TB incidence in rural areas will require further studies to identify high-risk populations and venues where local inhabitants congregate and transmit the infection.
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Affiliation(s)
- Zhuo Quan
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/ NHC/CAMS), School of Basic Medical Science, Fudan University, Shanghai, People's Republic of China
| | - Jiying Xu
- Institution for Tuberculosis Prevention and Control, Henan Provincial Center for Disease Control and Prevention, Zhengzhou, People's Republic of China
| | - Meng Li
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/ NHC/CAMS), School of Basic Medical Science, Fudan University, Shanghai, People's Republic of China
| | - Changyu Cheng
- Linzhou City Center for Disease Control and Prevention, Anyang, People's Republic of China
| | - Peierdun Mijiti
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/ NHC/CAMS), School of Basic Medical Science, Fudan University, Shanghai, People's Republic of China
| | - Qi Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, People's Republic of China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela
| | - Zhenhuan Ren
- Linzhou City Center for Disease Control and Prevention, Anyang, People's Republic of China
| | - Qian Gao
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/ NHC/CAMS), School of Basic Medical Science, Fudan University, Shanghai, People's Republic of China
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Rana Z, Leach M, Healey Akearok GK, Ukpatiku J, Umenwofor-Nweze N. A cross-sectional study exploring community perspectives on the impacts of COVID-19 in Nunavut and recommendations for a Holistic Inuit Qaujimajatuqangit approach to emergency response. Int J Circumpolar Health 2024; 83:2336680. [PMID: 38590216 PMCID: PMC11005875 DOI: 10.1080/22423982.2024.2336680] [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: 09/27/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
The goal of this study was to examine and address critical knowledge gaps and develop an understanding of both the positive and negative societal outcomes resulting from the public health measures associated with the COVID-19 pandemic in Nunavut and the interventions being undertaken to promote positive well-being. Data collection for this study included narrative, in-person interviews in Iqaluit, Rankin Inlet, Baker Lake, and Cambridge Bay between September 2022 and January 2023. A total of 70 participants were interviewed for this study. Community highlighted challenges, such as crowding and food insecurity, and concern for the collective wellbeing of the community. Strengths included financials supports, food sharing, and maintaining community connections over a distance. Recommendations included a focus on holistic health such as 1) public education and awareness about communicable disease, 2) financial supports, 3) housing, 4) access to healthcare, 5) focus on Inuit Qaujimajatuqangit, 6) mental-health and addiction supports, and 7) community spaces. Community members described both strengths and challenges they believe impacted their experiences and service delivery as well as recommendations for the future.
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Affiliation(s)
- Zoha Rana
- Qaujigiartiit Health Research Centre, Nunavut, Canada
| | - Meagan Leach
- Qaujigiartiit Health Research Centre, Nunavut, Canada
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Tschritter CM, van Coeverden de Groot P, Branigan M, Dyck M, Sun Z, Jenkins E, Buhler K, Lougheed SC. The geographic distribution, and the biotic and abiotic predictors of select zoonotic pathogen detections in Canadian polar bears. Sci Rep 2024; 14:12027. [PMID: 38797747 PMCID: PMC11128453 DOI: 10.1038/s41598-024-62800-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 05/21/2024] [Indexed: 05/29/2024] Open
Abstract
Increasing Arctic temperatures are facilitating the northward expansion of more southerly hosts, vectors, and pathogens, exposing naïve populations to pathogens not typical at northern latitudes. To understand such rapidly changing host-pathogen dynamics, we need sensitive and robust surveillance tools. Here, we use a novel multiplexed magnetic-capture and droplet digital PCR (ddPCR) tool to assess a sentinel Arctic species, the polar bear (Ursus maritimus; n = 68), for the presence of five zoonotic pathogens (Erysipelothrix rhusiopathiae, Francisella tularensis, Mycobacterium tuberculosis complex, Toxoplasma gondii and Trichinella spp.), and observe associations between pathogen presence and biotic and abiotic predictors. We made two novel detections: the first detection of a Mycobacterium tuberculosis complex member in Arctic wildlife and the first of E. rhusiopathiae in a polar bear. We found a prevalence of 37% for E. rhusiopathiae, 16% for F. tularensis, 29% for Mycobacterium tuberculosis complex, 18% for T. gondii, and 75% for Trichinella spp. We also identify associations with bear age (Trichinella spp.), harvest season (F. tularensis and MTBC), and human settlements (E. rhusiopathiae, F. tularensis, MTBC, and Trichinella spp.). We demonstrate that monitoring a sentinel species, the polar bear, could be a powerful tool in disease surveillance and highlight the need to better characterize pathogen distributions and diversity in the Arctic.
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Affiliation(s)
| | | | - Marsha Branigan
- Department of Environment and Climate Change, Government of the Northwest Territories, Inuvik, Northwest Territories, Canada
| | - Markus Dyck
- Department of Environment, Government of Nunavut, Igloolik, NT, Canada
| | - Zhengxin Sun
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Emily Jenkins
- Western College of Veterinary Medicine (WCVM), Saskatoon, SK, Canada
| | - Kayla Buhler
- Western College of Veterinary Medicine (WCVM), Saskatoon, SK, Canada
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Zhang X, Martinez E, Lam C, Crighton T, Sim E, Gall M, Donnan EJ, Marais BJ, Sintchenko V. Exploring programmatic indicators of tuberculosis control that incorporate routine Mycobacterium tuberculosis sequencing in low incidence settings: a comprehensive (2017-2021) patient cohort analysis. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2023; 41:100910. [PMID: 37808343 PMCID: PMC10550799 DOI: 10.1016/j.lanwpc.2023.100910] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/02/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
Background Routine whole genome sequencing of Mycobacterium tuberculosis has been implemented with increasing frequency. However, its value for tuberculosis (TB) control programs beyond individual case management and enhanced drug resistance detection has not yet been explored. Methods We analysed routine sequencing data of culture-confirmed TB cases notified between 1st January 2017 and 31st December 2021 in New South Wales (NSW), Australia. Genomic surveillance included evidence of local TB transmission, defined by single nucleotide polymorphism (SNP) clustering over a variable (0-25) SNP threshold, and drug resistance conferring mutations. Findings M. tuberculosis sequences from 1831 patients were examined, representing 64.8% of all notified TB cases and 96.2% of culture-confirmed cases. Applying a traditional 5-SNP cluster threshold identified 62 transmission clusters with 183 clustered cases; 101/183 (55.2%) had 0 SNP differences. Cluster assessment over a 5-year period, using a 5-SNP threshold, provided a comprehensive overview of likely recent transmission within NSW, Australia, as an indicator of local TB control. Genotypic drug susceptibility testing (DST) was highly concordant with phenotypic DST and provided a 6.8% increase in antimycobacterial resistance detection. Importantly, it detected mutations missed by routine molecular tests. Lineage 2 strains were more likely to be drug resistant (p < 0.0001) and locally transmitted if drug resistant (p < 0.0001). Interpretation Performing routine prospective WGS in a low incidence country like Australia, provides genomically informed programmatic indicators of local TB control. A rolling 5-year cluster assessment reflects epidemic containment and progress towards 'zero TB transmission'. Genomic DST also provides valuable information for clinical care and drug resistance surveillance. Funding NHMRC Centre for Research Excellence in Tuberculosis (www.tbcre.org.au) and NSW Health Prevention Research Support Program.
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Affiliation(s)
- Xiaomei Zhang
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Elena Martinez
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology - Western, Sydney, New South Wales, Australia
| | - Connie Lam
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Taryn Crighton
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology - Western, Sydney, New South Wales, Australia
| | - Eby Sim
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Mailie Gall
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Ellen J. Donnan
- New South Wales Tuberculosis Program, Health Protection NSW, Sydney, New South Wales, Australia
| | - Ben J. Marais
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology - Western, Sydney, New South Wales, Australia
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Smith JP, Cohen T, Dowdy D, Shrestha S, Gandhi NR, Hill AN. Quantifying Mycobacterium tuberculosis Transmission Dynamics Across Global Settings: A Systematic Analysis. Am J Epidemiol 2023; 192:133-145. [PMID: 36227246 PMCID: PMC10144641 DOI: 10.1093/aje/kwac181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/23/2022] [Accepted: 10/10/2022] [Indexed: 01/11/2023] Open
Abstract
The degree to which individual heterogeneity in the production of secondary cases ("superspreading") affects tuberculosis (TB) transmission has not been systematically studied. We searched for population-based or surveillance studies in which whole genome sequencing was used to estimate TB transmission and in which the size distributions of putative TB transmission clusters were enumerated. We fitted cluster-size-distribution data to a negative binomial branching process model to jointly infer the transmission parameters $R$ (the reproduction number) and the dispersion parameter, $k$, which quantifies the propensity of superspreading in a population (generally, lower values of $k$ ($<1.0$) suggest increased heterogeneity). Of 4,796 citations identified in our initial search, 9 studies from 8 global settings met the inclusion criteria (n = 5 studies of all TB; n = 4 studies of drug-resistant TB). Estimated $R$ values (range, 0.10-0.73) were below 1.0, consistent with declining epidemics in the included settings; estimated $k$ values were well below 1.0 (range, 0.02-0.48), indicating the presence of substantial individual-level heterogeneity in transmission across all settings. We estimated that a minority of cases (range, 2%-31%) drive the majority (80%) of ongoing TB transmission at the population level. Identifying sources of heterogeneity and accounting for them in TB control may have a considerable impact on mitigating TB transmission.
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Affiliation(s)
- Jonathan P Smith
- Correspondence to Dr. Jonathan Smith, Yale School of Public Health, Yale University, 60 College Street, New Haven, CT 06510 (e-mail: )
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Sharma MK, Janella D, McGurran A, Corbett C, Adam H, Akochy PM, Haldane D, MacKenzie H, Minion J, Needle R, Newberry C, Patterson M, Sekirov I, Tyrrell G, Soualhine H. Compilation of 10 Years of MIRU-VNTR Data: Canadian National Tuberculosis Laboratory's Experience. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:3505142. [PMID: 36046174 PMCID: PMC9424012 DOI: 10.1155/2022/3505142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/06/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022]
Abstract
Tuberculosis is a significant cause of morbidity worldwide and is a priority at the provincial and federal levels in Canada. It is known that tuberculosis transmission networks are complex and span many years as well as different jurisdictions and countries. MIRU-VNTR is a universal tuberculosis genotyping method that utilizes a 24-loci pattern and it has shown promise in identifying inter and intrajurisdictional clusters within Canada. MIRU-VNTR data collected over 10 years from the National Reference Centre for Mycobacteriology (NRCM) were analyzed in this study. Some clusters were unique to a single province/territory, while others spanned multiple provinces and/or territories in Canada. The use of a universal laboratory test can enhance contact tracing, provide geographical information on circulating genotypes, and hence, aid in tuberculosis investigation by public health. The housing of all data on one platform, technical ease of the method, easy exchange of data between jurisdictions, and strong collaboration with laboratories and surveillance units at the provincial and federal levels have the potential to identify possible outbreaks in real time.
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Affiliation(s)
- Meenu K. Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Debra Janella
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Alisa McGurran
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Cindi Corbett
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | | | | | - David Haldane
- Public Health Laboratory Network, Halifax, Nova Scotia, Canada
| | - Hope MacKenzie
- Atlantic Health Sciences Corporation, Saint John, New Brunswick, Canada
| | - Jessica Minion
- Saskatchewan Health Authority, Saskatoon, Saskatchewan, Canada
| | - Robert Needle
- Newfoundland and Labrador Public Health Laboratory, Saint John, Newfoundland, Canada
| | - Caroline Newberry
- Office of Chief Public Health Officer, Yellowknife, Northwest Territories, Canada
| | | | - Inna Sekirov
- BC Centre for Disease Control, Vancouver, British Columbia, Canada
| | | | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
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Bai Y, Shao C, Hao Y, Wang Y, Jin Y. Using Whole Genome Sequencing to Trace, Control and Characterize a Hospital Infection of IMP-4-Producing Klebsiella pneumoniae ST2253 in a Neonatal Unit in a Tertiary Hospital, China. Front Public Health 2021; 9:755252. [PMID: 34976919 PMCID: PMC8715938 DOI: 10.3389/fpubh.2021.755252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 11/15/2021] [Indexed: 12/31/2022] Open
Abstract
Background: The purpose of this study is to use whole genome sequencing (WGS) combined with epidemiological data to track a hospital infection of the carbapenem-resistant Klebsiella pneumoniae (CRKP), which affected 3 neonatal patients in the neonatal intensive care unit (NICU). Methods: The minimum inhibitory concentrations for the antimicrobial agents were determined according to the guidelines of the Clinical and Laboratory Standards Institute. Beta-lactamases were investigated using the polymerase chain reaction and DNA sequencing. The transferability of the plasmid was investigated by a conjugation experiment. The clonal relationships were evaluated using multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). WGS and single nucleotide polymorphisms (SNPs) analysis were performed on the CRKP isolates to investigate how the infection might progress. Results: Nine CRKP isolates were obtained from the NICU, seven from three patients, one from a duster cloth and one from the hand of a nurse, they all harbored blaIMP-4. Other resistance genes including blaKPC-2, blaIMP-4, blaSHV-1, blaTEM-1, blaCTX-M-15, and blaDHA-1 were also detected. PFGE analysis showed that IMP-4-producing K. pneumoniae were clonally related, and MLST assigned them to a new sequence type 2253. The SNP variations throughout the genome divided the 9 strains into three clades. Clade 1 comprised 7 strains (K1- K2 and K4-K8), whereas clade 2 and 3 consisted of only one strain each: K3 and K9, respectively.The sputum isolate K3 from patient 3 was the most distinct one differing from the other eight isolates by 239-275 SNPs. Conclusions: This is a report of using WGS to track a hospital infecion of IMP-4-producing K. pneumoniae ST2253 among neonates. Nosocomial surveillance systems are needed to limit the spread of the infection caused by these pathogens resulting from the environmental exposure in NICUs.
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Santos MDV, Barros MPS, Silveira-Filho VDM, Mendes-Marques CL, Lima AVA, Silva MVD, Leal-Balbino TC, Silva MDPCD, Paiva PMG, Oliveira MBMD. Genetic and Biochemical Diversity of Clinical Acinetobacter baumannii and Pseudomonas aeruginosa Isolates in a Public Hospital in Brazil. Microb Drug Resist 2020; 27:509-517. [PMID: 32882147 DOI: 10.1089/mdr.2020.0154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Life-threatening bacterial infections are a major concern in health care services worldwide. This retrospective study aimed to demonstrate genetic and biochemical diversity in isolates of Acinetobacter baumannii and Pseudomonas aeruginosa from a public hospital in Brazil. A total of 63 isolates collected from different sites of infection and hospital sectors were characterized, and their susceptibility profile to antibiotics was assessed for 18 drugs belonging to 8 antimicrobial categories using the automated BACTEC system. Genetic diversity was assessed using the multiple locus variable number tandem repeat analysis. Among the isolates of A. baumannii, 83% were classified as extensively drug resistant (XDR), and 17 genotypic profiles were identified. About 67% of P. aeruginosa isolates were susceptible to antimicrobials and were distributed into 37 genotypic profiles, revealing genetic heterogeneity. This study has demonstrated the multicolonization of investigated pathogens and the high frequency (95.8%) of multidrug-resistant and XDR, as well as high genetic diversity, among the isolates supporting the continuous need to monitor these species in the hospital environment.
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Affiliation(s)
| | | | | | | | | | - Marcia Vanusa da Silva
- Department of Biochemistry, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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