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Valiatti TB, Nunes PHS, Santos FF, Cayô R, Marcelino IN, Alberto-Lei F, Varjão HA, Gales AC, Gomes TAT. Detection of virulent Klebsiella pneumoniae strains causing intestinal and extraintestinal infections during the 80s and 90s in Brazil. Braz J Microbiol 2024:10.1007/s42770-024-01502-y. [PMID: 39225874 DOI: 10.1007/s42770-024-01502-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
Klebsiella pneumoniae is an important pathogen that causes several human infections, which is currently among the main bacterial species of clinical importance. Given the importance of understanding the characteristics of this pathogen and its evolutionary aspects, in this study, we sought to characterize strains of K. pneumoniae recovered in the 1980s and 1990s in São Paulo, Brazil. Our analyses included 48 strains recovered from diarrheagenic stools and extraintestinal infections. These strains were submitted to screening for virulence and ESβL-encoding genes, antimicrobial susceptibility tests, biofilm formation, and hypermucosity and hemolytic activity tests. Our results revealed that among the studied virulence genes, the most frequent were entB (100%), followed by iutA (100%), mrkD (98%), and ycfM (72%). Phenotypic tests revealed that the strains were non- hemolytic, and two strains were positive for the hypermucoviscosity phenotype but did not have the genetic markers associated with this phenotype. Furthermore, 17% of the isolates proved to be strong biofilm producers. Antimicrobial susceptibility testing demonstrated that most strains were susceptible to the tested antimicrobials, with the exception of five isolates that produced CTX-M-2. Our findings indicate that the collection of strains studied showed variability in virulence factors, as well as biofilm production. Still, a minority of the strains showed clinically significant resistance mechanisms. As far as we know, this is the oldest collection of K. pneumoniae studied in the country.Keywords: Bacterial virulence; Ancient bacterial strains; Enterobacterales; Bacterial infection; Diarrhea.
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Affiliation(s)
- Tiago Barcelos Valiatti
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil.
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil.
- Faculdade de Educação de Jaru (FIMCA Jaru), Grupo Rondoniense de Pesquisa em Ciências da Saúde, Jaru, RO, Brazil.
| | - Pedro Henrique Soares Nunes
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Fernanda Fernandes Santos
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Rodrigo Cayô
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
- Laboratory of Environmental Antimicrobial Resistance (LEARN), Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Universidade Federal de São Paulo (UNIFESP), Diadema, SP, Brazil
| | - Ingrid Nayara Marcelino
- Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Felipe Alberto-Lei
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Haian Araujo Varjão
- Faculdade de Educação de Jaru (FIMCA Jaru), Grupo Rondoniense de Pesquisa em Ciências da Saúde, Jaru, RO, Brazil
| | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
- Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Tânia Aparecida Tardelli Gomes
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil.
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Bighi N, Freitas F, Morgado S, Cipriano R, Vicente AC, Fonseca ÉL. Deciphering the accessory genome of a novel Klebsiella pneumoniae lineage in the Brazilian Amazon region and its potential contribution to the emergence of a high-risk clone. J Antimicrob Chemother 2024; 79:1709-1711. [PMID: 38742712 DOI: 10.1093/jac/dkae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Affiliation(s)
- Nathália Bighi
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
| | - Fernanda Freitas
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
| | - Sérgio Morgado
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Ana Carolina Vicente
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
| | - Érica L Fonseca
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
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Mourão J, Ribeiro-Almeida M, Novais C, Magalhães M, Rebelo A, Ribeiro S, Peixe L, Novais Â, Antunes P. From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production. Microbiol Spectr 2023; 11:e0138623. [PMID: 37428073 PMCID: PMC10434174 DOI: 10.1128/spectrum.01386-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Concerns about colistin-resistant bacteria in animal food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae in the whole poultry production chain needs clarification. We assessed colistin-resistant and copper-tolerant K. pneumoniae occurrence in chickens raised with inorganic and organic copper formulas from 1-day-old chicks to meat (7 farms from 2019 to 2020), after long-term colistin withdrawal (>2 years). Clonal diversity and K. pneumoniae adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken flocks (75%) carried K. pneumoniae at early and preslaughter stages, with a significant decrease (P < 0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative K. pneumoniae were observed among fecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant (81%; silA and pcoD positive and with a MICCuSO4 of ≥16 mM) isolates. WGS revealed accumulation of colistin resistance-associated mutations and F type multireplicon plasmids carrying antibiotic resistance and metal/copper tolerance genes. The K. pneumoniae population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146, and ST392-KL27 and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken production as a reservoir/source of clinically relevant K. pneumoniae lineages and genes with potential risk to humans through food and/or environmental exposure. Despite the limited mcr spread due to the long-term colistin ban, this action was ineffective in controlling colistin-resistant/mcr-negative K. pneumoniae, regardless of feed. This study provides crucial insights into the persistence of clinically relevant K. pneumoniae in the poultry production chain and highlights the need for continued surveillance and proactive food safety actions within a One Health perspective. IMPORTANCE The spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically relevant Klebsiella pneumoniae throughout the poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative K. pneumoniae in chicken flocks, regardless of inorganic and organic copper formulas use and a long-term colistin ban. Despite the high K. pneumoniae isolate diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human K. pneumoniae exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in the food industry and policymakers tasked with regulating food safety.
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Affiliation(s)
- Joana Mourão
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Marisa Ribeiro-Almeida
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Mafalda Magalhães
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
- ESS, Polytechnic of Porto, Porto, Portugal
| | - Sofia Ribeiro
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ângela Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
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Kowalczyk J, Czokajło I, Gańko M, Śmiałek M, Koncicki A. Identification and Antimicrobial Resistance in Klebsiella spp. Isolates from Turkeys in Poland between 2019 and 2022. Animals (Basel) 2022; 12:ani12223157. [PMID: 36428385 PMCID: PMC9686990 DOI: 10.3390/ani12223157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022] Open
Abstract
One of the important problems in poultry production is bacterial infections and increasing resistance to antibiotics. The increasing incidence of multidrug-resistant bacteria is a major challenge for physicians and veterinarians and considerably limits treatment options. This study was undertaken in order to assess the prevalence and antibiotic resistance of Klebsiella spp. strains isolated from turkeys sampled from 2019 to 2022 in Poland. The material for study consisted of clinical samples taken during routine monitoring and microbiological identification testing at commercial poultry farms. From all 507 isolates of Klebsiella, 95% were identified by MALDI-TOF (Matrix-Assisted Laser Desorption - Ionisation-Time of Flight) as Klebsiella pneumonia, 2% were Klebsiella oxytoca, 2% Klebsiella variicola, or unidentified (1%). All isolated Klebsiella strains were tested for antimicrobial susceptibility by disk diffusion. The results of our study indicated that colistin, neomycin, florfenicol and amoxicillin/clavulanic acid were the most effective against the Klebsiella spp. isolated from turkeys. In addition, the results show a decrease in the number of multi-resistant Klebsiella spp. strains between 2019 and 2021.
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Affiliation(s)
- Joanna Kowalczyk
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury, Oczapowskiego 13, 10-719 Olsztyn, Poland
- Correspondence: ; Tel.: +48-89-523-38-11
| | - Ilona Czokajło
- SLW Biolab Veterinary Laboratory, ul. Grunwaldzka 62, 14-100 Ostróda, Poland
| | - Marta Gańko
- SLW Biolab Veterinary Laboratory, ul. Grunwaldzka 62, 14-100 Ostróda, Poland
| | - Marcin Śmiałek
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury, Oczapowskiego 13, 10-719 Olsztyn, Poland
- SLW Biolab Veterinary Laboratory, ul. Grunwaldzka 62, 14-100 Ostróda, Poland
| | - Andrzej Koncicki
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury, Oczapowskiego 13, 10-719 Olsztyn, Poland
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5
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Sahin S, Mogulkoc MN, Kürekci C. Disinfectant and heavy metal resistance profiles in extended spectrum β-lactamase (ESBL) producing Escherichia coli isolates from chicken meat samples. Int J Food Microbiol 2022; 377:109831. [PMID: 35843029 DOI: 10.1016/j.ijfoodmicro.2022.109831] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 12/01/2022]
Abstract
Biocidal compounds are frequently used as disinfectants in poultry industry and their widespread usage has risen concern due to the co-selection and persistence of antimicrobial resistance among bacteria. In this study, extended spectrum β-lactamase producing (ESBL) Escherichia coli isolates (n = 60) obtained from chicken meat were characterized by Pulsed Field Gel Electrophoresis (PFGE) and further tested for disinfectant and heavy metal resistance phenotypically and genotypically. Plasmid replicon types of these isolates were also determined. ESBL producing E. coli isolates were found to be resistant to ciprofloxacin (48.3 %) and gentamicin (15 %). The majority of these isolates (46.5 %) carried blaCTX-M-55 gene. The isolates showed higher minimal inhibitory concentrations to cetylpyridinium chloride (90 %), cetyltrimethylammonium bromide (50 %), hexadecyltrimethylammonium bromide (46.7 %), triclosan (38.3 %), benzalkonium chloride (28.3 %), chlorhexidine (21.7 %), acriflavine (3.3 %), benzethonium chloride (1.7 %) and N-alkyl dimethyl benzyl ammonium chloride (1.7 %), but 18.3 % of the isolates were resistant to triclosan. Of the quaternary ammonium compounds (QACs) tolerance genes, mdfA, sugE(c), ydgE and ydgF were most present in all isolates, but the qacE, qacG, oqxA and oqxB genes were not detected. Of genes mediating the heavy metal resistance, the zitB gene was detected in all isolates, whereas the copA and cueO genes were detected in 96.67 % and 95 % of isolates, respectively. The IncFIB plasmid was commonly present (93.3 %) in ESBL producing E. coli isolates. Consequently, given the detection of genes mediating disinfectant and heavy metal resistance commonly in ESBL producing E. coli isolates as well as high rate of MICs against disinfectant compounds, the use of QACs for decontamination of the facilities may not be as effective as expected in poultry sector in Turkey.
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Affiliation(s)
- Seyda Sahin
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Sivas Cumhuriyet University, Sivas 58140, Turkey.
| | - Mahmut Niyazi Mogulkoc
- Department of Microbiology, Faculty of Veterinary Medicine, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Cemil Kürekci
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay 31030, Turkey
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Sanni AO, Onyango J, Usman A, Abdulkarim LO, Jonker A, Fasina FO. Risk Factors for Persistent Infection of Non-Typhoidal Salmonella in Poultry Farms, North Central Nigeria. Antibiotics (Basel) 2022; 11:antibiotics11081121. [PMID: 36009991 PMCID: PMC9405283 DOI: 10.3390/antibiotics11081121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/13/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
Salmonellosis is a bacterial zoonosis causing an array of health conditions. Non-typhoidal salmonellosis (NTS) has a discrete adaptation to certain animals; in poultry, pullorum and fowl typhoid are its primary disease manifestations. The diseases are prevalent in Nigerian poultry and have been well-studied in Nigeria, but less so in North Central Nigeria (NCN). Using field sampling, laboratory methods and a semi-structured questionnaire for 1000 poultry farms in NCN, we explored the incidence and risk factors for the persistence of NTS infection in poultry. Approximately 41.6% of the farms had experienced NTS over the last 18 months. Farm experience of NTS moderately predicted awareness of salmonellosis. Increasing stock in smallholder farms, self-mixing of concentrate on the farm, usage of stream water, pen odour, non-adherence and partial adherence of farms to recommended poultry vaccination against pullorum and fowl typhoid and lack of and non-adherence to biosecurity were identified risk factors that increased the odds of NTS infection in poultry. Antibiotic use practice may have reduced the isolation rate of NTS, yet NTS continues to challenge poultry farms in Nigeria. Identified risk practices must be mitigated intentionally and biosecurity and hygiene must be improved to reduce the burden of NTS.
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Affiliation(s)
- Abdullahi O. Sanni
- Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa
- Agro-Processing, Productivity Enhancement and Livelihood Improvement Support (APPEALS) Project, Lokoja 260101, Kogi State, Nigeria
| | - Joshua Onyango
- Harper and Keele Veterinary School, Harper Adams University, Newport TF10 8NB, UK
| | - Abdulkadir Usman
- Department of Animal Production, Federal University of Technology, Minna 920101, Niger, Nigeria
| | - Latifah O. Abdulkarim
- Agro-Processing, Productivity Enhancement and Livelihood Improvement Support (APPEALS) Project, Lokoja 260101, Kogi State, Nigeria
| | - Annelize Jonker
- Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa
| | - Folorunso O. Fasina
- Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa
- ECTAD Food and Agriculture Organization of the United Nations, Nairobi 00100, Kenya
- Correspondence: or ; Tel.: +254-111-3232-70
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Zong S, Xu D, Zheng X, Zaeim D, Wang P, Han J, Qu D. The diversity in antimicrobial resistance of MDR Enterobacteriaceae among Chinese broiler and laying farms and two mcr-1 positive plasmids revealed their resistance-transmission risk. Front Microbiol 2022; 13:912652. [PMID: 35992687 PMCID: PMC9387725 DOI: 10.3389/fmicb.2022.912652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
This research aimed to investigate the microbial composition and diversity of antimicrobial resistance genes (ARGs) found in Chinese broiler and layer family poultry farms. We focused on the differences in resistance phenotypes and genotypes of multidrug-resistant Enterobacteriaceae (MDRE) isolated from the two farming environments and the existence and transmissibility of colistin resistance gene mcr-1. Metagenomic analysis showed that Firmicutes and Bacteroides were the dominant bacteria in broiler and layer farms. Many aminoglycoside and tetracycline resistance genes were accumulated in these environments, and their absolute abundance was higher in broiler than in layer farms. A total of 526 MDRE were isolated with a similar distribution in both farms. The results of the K-B test showed that the resistance rate to seven antimicrobials including polymyxin B and meropenem in broiler poultry farms was significantly higher than that in layer poultry farms (P ≤ 0.05). PCR screening results revealed that the detection rates of mcr-1, aph(3’)Ia, aadA2, blaoxa–1, blaCTX–M, fosB, qnrD, sul1, tetA, and catA1 in broiler source MDRE were significantly higher than those in layers (P ≤0.05). A chimeric plasmid p20432-mcr which carried the novel integron In1866 was isolated from broiler source MDRE. The high frequency of conjugation (10–1 to 10–3) and a wide range of hosts made p20432-mcr likely to play an essential role in the high detection rate of mcr-1, aph(3’)-Ia, and aadA2 in broiler farms. These findings will help optimize disinfection and improve antimicrobial-resistant bacteria surveillance programs in poultry farms, especially broilers.
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Affiliation(s)
- Shuaizhou Zong
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Dingting Xu
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiner Zheng
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Davood Zaeim
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Peng Wang
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Jianzhong Han
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Daofeng Qu
- Key Laboratory of Food Quality and Safety, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
- *Correspondence: Daofeng Qu,
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8
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Savin M, Bierbaum G, Schmithausen RM, Heinemann C, Kreyenschmidt J, Schmoger S, Akbaba I, Käsbohrer A, Hammerl JA. Slaughterhouse wastewater as a reservoir for extended-spectrum β-lactamase (ESBL)-producing, and colistin-resistant Klebsiella spp. and their impact in a "One Health" perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150000. [PMID: 34517324 DOI: 10.1016/j.scitotenv.2021.150000] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 05/28/2023]
Abstract
Klebsiella spp. are ubiquitous bacteria capable of colonizing humans and animals, and sometimes leading to severe infections in both. Due to their high adaptability against environmental/synthetic conditions as well as their potential in aquiring antimicrobial/metal/biocide resistance determinants, Klebsiella spp. are recognized as an emerging threat to public health, worldwide. Currently, scarce information on the impact of livestock for the spread of pathogenic Klebsiella spp. is available. Thus, the phenotypic and genotypic properties of extended-spectrum β-lactamase-producing, and colistin-resistant Klebsiella strains (n = 185) from process- and wastewater of two poultry and pig slaughterhouses as well as their receiving municipal wastewater treatment plants (mWWTPs) were studied to determine the diversity of isolates that might be introduced into the food-production chain or that are released into the environment by surviving the wastewater treatment. Selectively-isolated Klebsiella spp. from slaughterhouses including effluents and receiving waterbodies of mWWTPs were assigned to various lineages, including high-risk clones involved in human outbreaks, and exhibited highly heterogeneous antibiotic-resistance patterns. While isolates originating from poultry slaughterhouses showed the highest rate of colistin resistance (32.4%, 23/71), carbapenem-resistant Klebsiella spp. were only detected in mWWTP samples (n = 76). The highest diversity of resistance genes (n = 77) was detected in Klebsiella spp. from mWWTPs, followed by isolates from pig (n = 56) and poultry slaughterhouses (n = 52). Interestingly, no carbapenemase-encoding genes were detected and mobile colistin resistance genes were only obeserved in isolates from poultry and pig slaughterhouses. Our study provides in-depth information into the clonality of livestock-associated Klebsiella spp. and their determinants involved in antimicrobial resistance and virulence development. On the basis of their pathogenic potential and clinical importance there is a potential risk of colonization and/or infection of wildlife, livestock and humans exposed to contaminated food and/or surface waters.
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Affiliation(s)
- Mykhailo Savin
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, Germany; Institute of Animal Sciences, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | | | | | - Judith Kreyenschmidt
- Institute of Animal Sciences, University of Bonn, Bonn, Germany; Hochschule Geisenheim University, Department of Fresh Produce Logistics, Geisenheim, Germany
| | - Silvia Schmoger
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Inna Akbaba
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annemarie Käsbohrer
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany; Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, AT-1210 Vienna, Austria
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.
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9
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Cardozo MV, Liakopoulos A, Brouwer M, Kant A, Pizauro LJL, Borzi MM, Mevius D, de Ávila FA. Occurrence and Molecular Characteristics of Extended-Spectrum Beta-Lactamase-Producing Enterobacterales Recovered From Chicken, Chicken Meat, and Human Infections in Sao Paulo State, Brazil. Front Microbiol 2021; 12:628738. [PMID: 34239503 PMCID: PMC8259509 DOI: 10.3389/fmicb.2021.628738] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
This study aimed to investigate the phylogenetic diversity and epidemiology of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae from chicken, chicken meat, and human clinical isolates in Sao Paolo, Brazil, and characterize their respective ESBL-encoding plasmids. Three hundred samples from chicken cloaca, chicken meat, and clinical isolates were phenotypically and genotypically assessed for ESBL resistance. Isolates were identified by MALDI TOF-MS and further characterized by MLST analysis and phylogenetic grouping. ESBL genes were characterized and their location was determined by I-Ceu-I-PFGE and Southern blot, conjugation, transformation, and PCR-based replicon typing experiments. Thirty-seven ESBL-producing isolates (28 E. coli and 9 K. pneumoniae) that were positive for the bla CTX-M-1 or bla CTX-M-2 gene groups were obtained. Two isolates were negative in the transformation assay, and the chromosomal location of the genes was deduced by Southern blot. The bla CTX-M genes identified were carried on plasmid replicon-types X1, HI2, N, FII-variants, I1 and R. The E. coli isolates belonged to nine sequence types, while the K. pneumoniae isolates belonged to four sequence types. The E. coli isolates belonged to phylotype classification groups A, B1, D, and F. This study demonstrated that isolates from cloacal swabs, chicken meat, and human feces had genetic diversity, with a high frequency of bla CTX-M-15 among chickens, chicken meat, and human feces. Thus, this reinforces the hypothesis that chickens, as well as their by-products, could be an important source of transmission for ESBL-producing pathogens to humans in South America.
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Affiliation(s)
- Marita Vedovelli Cardozo
- Department of Veterinary Pathology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Apostolos Liakopoulos
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Michael Brouwer
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Arie Kant
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Lucas José Luduvério Pizauro
- Department of Tecnology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Mariana Monezi Borzi
- Department of Veterinary Pathology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Fernando Antonio de Ávila
- Department of Veterinary Pathology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
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10
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Elmonir W, Abd El-Aziz NK, Tartor YH, Moustafa SM, Abo Remela EM, Eissa R, Saad HA, Tawab AA. Emergence of Colistin and Carbapenem Resistance in Extended-Spectrum β-Lactamase Producing Klebsiella pneumoniae Isolated from Chickens and Humans in Egypt. BIOLOGY 2021; 10:biology10050373. [PMID: 33926062 PMCID: PMC8146310 DOI: 10.3390/biology10050373] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/26/2022]
Abstract
Simple Summary Carbapenems and colistin are reserved as the last-resort treatments of multidrug-resistant (MDR) infections in humans. Consequently, the emergence of carbapenem and colistin-resistant Klebsiella pneumoniae (K. pneumoniae) in poultry, contact workers and hospitalized patients is of grave concern for therapeutic options, and no data are available supporting this assumption on a regional or countrywide scale. We investigated the frequency and typing of extended-spectrum β-lactamase (ESBL) and carbapenemase-producing K. pneumoniae (ESBLK and CPK) in hospitalized patients, chickens from 10 poultry farms and their environment (water, food and litter) and farm workers in Egypt. All isolates from patients (13/90, 14.4%), workers (5/22, 22.7%), chickens (9/100, 9%) and the environment (10/60, 16.7%) harbored a single or multiple β-lactamase genes, blaSHV, blaTEM, blaCTX-M1 and blaOXA-1, often in combination with carbapenemase genes (blaVIM, blaNDM-1 or blaIMP; 45.9%), the mcr-1 gene (18.9%) or both (13.5%). Enterobacterial repetitive intergenic consensus (ERIC)-PCR genotyping highlighted potential inter and intraspecies clonal dissemination in the study area. The increased frequency and genetic relatedness of ESBLK and CPK from chickens and humans pose a public health threat that urges more prudent use of antimicrobials in chicken farms to avoid the propagation and expansion of both ESBLK and CPK from the chicken sources to humans. Abstract This study investigated the frequency of carbapenem and colistin resistance in ESBL-producing K. pneumoniae (ESBLK) isolates recovered from chickens and their environment, contact farm workers and hospitalized patients in Egypt. Further, the phenotypic and genotypic relationships between the community and hospital-acquired K. pneumoniae isolates in the same geographical area were investigated. From 272 total samples, 37 (13.6%) K. pneumoniae isolates were identified, of which 20 (54.1%) were hypervirulent. All isolates (100%) were multidrug-resistant (MDR) with multiple antibiotic resistance (MAR) indices ranging from 0.19 to 0.94. Colistin-resistant isolates (18.9%) displayed colistin MIC values >2 μg/mL, all harbored the mcr-1 gene. All isolates from patients (13/90, 14.4%), workers (5/22, 22.7%), chickens (9/100, 9%) and the environment (10/60, 16.7%) harbored a single or multiple β-lactamase genes, blaSHV, blaTEM, blaCTX-M1 and blaOXA-1, often in combination with carbapenemase genes (blaVIM, blaNDM-1 or blaIMP; 45.9%), the mcr-1 gene (18.9%) or both (13.5%). Enterobacterial repetitive intergenic consensus (ERIC)–PCR genotyping revealed 24 distinct ERIC types (ETs) with a discrimination index of 0.961. Six ETs showed clusters of identical isolates from chicken and human sources. The increased frequency and genetic relatedness of ESBLK and carbapenemase-producing K. pneumoniae (CPK) from chickens and humans pose a public health threat that urge more prudent use of antimicrobials in chicken farms to avoid the propagation and expansion of both ESBLK and CPK from the chicken sources to humans.
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Affiliation(s)
- Walid Elmonir
- Department of Hygiene and Preventive Medicine (Zoonoses), Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Norhan K Abd El-Aziz
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Yasmine H Tartor
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Samar M Moustafa
- Department of Zoonoses, Faculty of Veterinary Medicine, Benha University, Benha 13518, Egypt
| | - Etab M Abo Remela
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
- Department of Biology, College of Science, Taibah University, Madina 42353, Saudi Arabia
| | - Radwa Eissa
- Department of Microbiology and Immunology, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
| | - Hosam A Saad
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Abdel Tawab
- Department of Microbiology, Faculty of Medicine, Al Azhar University, Cairo 11884, Egypt
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11
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Du FL, Huang QS, Wei DD, Mei YF, Long D, Liao WJ, Wan LG, Liu Y, Zhang W. Prevalence of Carbapenem-Resistant Klebsiella pneumoniae Co-Harboring blaKPC-Carrying Plasmid and pLVPK-Like Virulence Plasmid in Bloodstream Infections. Front Cell Infect Microbiol 2021; 10:556654. [PMID: 33777826 PMCID: PMC7996060 DOI: 10.3389/fcimb.2020.556654] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/31/2020] [Indexed: 12/22/2022] Open
Abstract
This study aimed to characterize carbapenem-resistant Klebsiella pneumoniae (CR-KP) co-harboring bla KPC-2-carrying plasmid and pLVPK-like virulence plasmid. Between December 2017 and April 2018, 24 CR-KP isolates were recovered from 24 patients with bacteremia. The mortality was 66.7%. Pulsed-field gel electrophoresis and multilocus sequence typing results indicated four clusters, of which cluster A (n = 21, 87.5%) belonged to ST11 and the three remaining isolates (ST412, ST65, ST23) had different pulsotypes (cluster B, C, D). The bla KPC-2-carrying plasmids all belonged to IncFIIK type, and the size ranged from 100 to 390 kb. Nineteen strains (79.2%) had a 219-kb virulence plasmid possessed high similarity to pLVPK from CG43 with serotype K2. Two strains had a 224-kb virulence plasmid resembled plasmid pK2044 from K. pneumoniae NTUH-K2044(ST23). Moreover, three strains carried three different hybrid resistance- and virulence-encoding plasmids. Conjugation assays showed that both bla KPC-2 and rmpA2 genes could be successfully transferred to E. coli J53 in 62.5% of the strains at frequencies of 4.5 × 10-6 to 2.4 × 10-4, of which three co-transferred bla KPC-2 along with rmpA2 in large plasmids. Infection assays in the Galleria mellonella model demonstrated the virulence level of these isolates was found to be consistently higher than that of classic Klebsiella pneumoniae. In conclusion, CR-KP co-harboring bla KPC-2-carrying plasmid and pLVPK-like virulence plasmid were characterized by multi-drug resistance, enhanced virulence, and transferability, and should, therefore, be regarded as a real superbug that could pose a serious threat to public health. Hence, heightened efforts are urgently needed to avoid its co-transmission of the virulent plasmid (gene) and resistant plasmid (gene) in clinical isolates.
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Affiliation(s)
- Fang-Ling Du
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Qi-Sen Huang
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Dan-Dan Wei
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Yan-Fang Mei
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Dan Long
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Wen-Jian Liao
- Department of Respiratory, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - La-Gen Wan
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Yang Liu
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Wei Zhang
- Department of Respiratory, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
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12
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Kakooza S, Munyiirwa D, Ssajjakambwe P, Kayaga E, Tayebwa DS, Ndoboli D, Basemera L, Nabatta E, Tumwebaze MA, Kaneene JB. Epidemiological Dynamics of Extended-Spectrum β-Lactamase- or AmpC β-Lactamase-Producing Escherichia coli Screened in Apparently Healthy Chickens in Uganda. SCIENTIFICA 2021; 2021:3258059. [PMID: 34589246 PMCID: PMC8476277 DOI: 10.1155/2021/3258059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/17/2021] [Indexed: 05/05/2023]
Abstract
The dynamics of extended-spectrum β-lactamase- (ESBL-) and AmpC β-lactamase-producing bacteria (which are deadly groups of antimicrobial-resistant bacteria) have not been well understood in developing countries. This raises major concerns to antimicrobial resistance (AMR) control. We investigated the prevalence and factors linked to the fecal carriage of ESBL- or AmpC-producing Escherichia coli (ESBL-/AmpC-EC) in commercial chickens. Cloacal swabs from 400 birds were sampled and submitted to the Central Diagnostic Laboratory for ESBL-/AmpC-EC screening by culture methods using MacConkey agar supplemented with cefotaxime. Epidemiological data were collected using a structured questionnaire and plausible risk factor analyses prepared by R software using X 2 test and logistic regression modeling. Results showed that the prevalence of ESBL-/AmpC-EC was 17.5%. Univariable screening hypothesized that carriage was probably influenced by a type of commercial chicken, geographical location, age group, flock size, and housing system (p < 0.05). Modeling exposed that broiler birds were at a higher risk of being ESBL-/AmpC-EC carriers (COR = 9.82, CI = 3.85-25.07). Birds from Wakiso Town Council (COR = 4.89, CI = 2.04-11.72) and flocks of 700-1200 birds were also at a higher risk of harboring ESBL-/AmpC-EC (COR = 2.41, CI = 1.11-5.23). Birds aged 4 months and below were more susceptible to ESBL-/AmpC-EC carriage compared with those aged 1 month and below being 6.33 times (CI = 1.65-24.35) likely to be carriers. The occurrence of ESBL-/AmpC-EC in flocks suggests possible treatment failures while managing colibacillosis. Consequently, injudicious antimicrobial use should be replaced with an accurate diagnosis by bacterial culture and sensitivity testing so as to circumvent AMR emergence, spread, and associated losses.
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Affiliation(s)
- Steven Kakooza
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
- Vétérinaires Sans Frontières Germany, Kampala, Uganda
- Novel Minds Science Plexus, Kampala, Uganda
| | - Damien Munyiirwa
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
| | - Paul Ssajjakambwe
- Department of Veterinary Pharmacy, Clinics and Comparative Medicine, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
| | - Edrine Kayaga
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
| | - Dickson Stuart Tayebwa
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
| | - Dickson Ndoboli
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
| | - Loreen Basemera
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
| | - Esther Nabatta
- Infectious Diseases Institute, College of Health Sciences Makerere University, Kampala, Uganda
| | - Maria Agnes Tumwebaze
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Bio-Security Makerere University, Kampala, Uganda
| | - John Baligwamunsi Kaneene
- Michigan State University, Center for Comparative Epidemiology, 736 Wilson Road, Room A-109, East Lansing, MI 48824, USA
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13
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Wales A, Davies R. Review of hatchery transmission of bacteria with focus on Salmonella, chick pathogens and antimicrobial resistance. WORLD POULTRY SCI J 2020. [DOI: 10.1080/00439339.2020.1789533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Andrew Wales
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Robert Davies
- Department of Bacteriology and Food Safety, Animal and Plant Health Agency (APHA – Weybridge), Addlestone, UK
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14
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Zhou Y, Li Y, Zhang L, Wu Z, Huang Y, Yan H, Zhong J, Wang LJ, Abdullah HM, Wang HH. Antibiotic Administration Routes and Oral Exposure to Antibiotic Resistant Bacteria as Key Drivers for Gut Microbiota Disruption and Resistome in Poultry. Front Microbiol 2020; 11:1319. [PMID: 32733394 PMCID: PMC7358366 DOI: 10.3389/fmicb.2020.01319] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/25/2020] [Indexed: 01/05/2023] Open
Abstract
Previous studies have identified oral administration of antibiotics and gut-impacting drugs as critical drivers for fecal antibiotic resistance (AR) and microbiome disruption in lab mice, but the practical implications of these findings have yet to be validated in hosts nurtured in conventional environment. Using ampicillin (Amp) as a way to extrapolate the general effect of antibiotics, this project examined the impact of drug administration routes on fecal microbiota and resistome using poultry raised in a teaching farm. AR genes were found to be abundant in the feces of young Leghorn chicks without previous antibiotic treatment. In chickens seeded with bla CMY-2 + Escherichia coli, 300 mg/kg body weight of Amp was orally administered for 5 days. This led to the fecal microbiota switching from Firmicutes occupied (95.60 ± 2.62%) and Lactobacillus rich, to being dominated by Proteobacteria (70.91 ± 28.93%), especially Escherichia/Shigella. However, when Amp was given via muscle injection, Firmicutes was mostly retained (i.e., from 83.6 ± 24.4% pre- to 90.4 ± 15.2% post-treatment). In control chickens without seeding with bla CMY-2 + E. coli, oral Amp also led to the increase of Proteobacteria, dominated by Klebsiella and Escherichia/Shigella, and a reduction of Firmicutes. Specifically within Firmicutes, Enterococcus, Clostridium, etc. were enriched but Lactobacillus was diminished. The fecal resistome including Ampr genes was more abundant in chickens receiving oral Amp than those treated with muscle injection, but the difference was primarily within 1 log. The data illustrated that both drug administration routes and pre-existing gut microbiota have profound impacts on gut microbiome disruption when antibiotic treatment is given. In hosts nurtured in a conventional environment, drug administration route has the most evident impact on gut microbiota rather than the size of the targeted bla CMY-2 + gene pool, likely due to the pre-existing bacteria that are (i) less susceptible to Amp, and/or (ii) with Ampr- or multidrug resistance-encoding genes other than bla CMY-2 +. These results demonstrated the critical interplay among drug administration routes, microbiota seeded through the gastrointestinal tract, AR, gut microbiota disruption, and the rise of common opportunistic pathogens in hosts. The potential implications in human and animal health are discussed.
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Affiliation(s)
- Yang Zhou
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu Li
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
| | - Lu Zhang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science and Engineering of Technology, Guangzhou, China
| | - Zuowei Wu
- College of Veterinary Preventive Medicine, Iowa State University, Ames, IA, United States
| | - Ying Huang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - He Yan
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science and Engineering of Technology, Guangzhou, China
| | - Jiang Zhong
- Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Ju Wang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
| | - Hafiz M Abdullah
- Department of Animal Science Poultry Facility, OARDC, Wooster, OH, United States
| | - Hua H Wang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
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15
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Gona F, Comandatore F, Battaglia S, Piazza A, Trovato A, Lorenzin G, Cichero P, Biancardi A, Nizzero P, Moro M, Cirillo DM. Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis. Microb Genom 2020; 6:e000347. [PMID: 32149598 PMCID: PMC7276701 DOI: 10.1099/mgen.0.000347] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/13/2020] [Indexed: 12/19/2022] Open
Abstract
In this work we compared the most frequently used Klebsiella pneumoniae typing methods: PFGE, cgMLST and coreSNP. We evaluated the discriminatory power of the three methods to confirm or exclude nosocomial transmission on K. pneumoniae strains isolated from January to December 2017, in the framework of the routine surveillance for multidrug-resistant organisms at the San Raffaele Hospital, in Milan. We compared the results of the different methods to the results of epidemiological investigation. Our results showed that cgMLST and coreSNP are more discriminant than PFGE, and that both approaches are suitable for transmission analyses. cgMLST appeared to be inferior to coreSNP in the K. pneumoniae CG258 phylogenetic reconstruction. Indeed, we found that the phylogenetic reconstruction based on cgMLST genes wrongly clustered ST258 clade1 and clade2 strains, conversely properly assigned by coreSNP approach. In conclusion, this study provides evidences supporting the reliability of both cgMLST and coreSNP for hospital surveillance programs and highlights the limits of cgMLST scheme genes for phylogenetic reconstructions.
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Affiliation(s)
- Floriana Gona
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, Milan, Italy
| | - Simone Battaglia
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Aurora Piazza
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, Milan, Italy
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Lorenzin
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Institute of Microbiology and Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Paola Cichero
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anna Biancardi
- Infection Control, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Nizzero
- Infection Control, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Moro
- Infection Control, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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16
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Savin M, Bierbaum G, Hammerl JA, Heinemann C, Parcina M, Sib E, Voigt A, Kreyenschmidt J. ESKAPE Bacteria and Extended-Spectrum-β-Lactamase-Producing Escherichia coli Isolated from Wastewater and Process Water from German Poultry Slaughterhouses. Appl Environ Microbiol 2020; 86:e02748-19. [PMID: 32033950 PMCID: PMC7117925 DOI: 10.1128/aem.02748-19] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
The wastewater of livestock slaughterhouses is considered a source of antimicrobial-resistant bacteria with clinical relevance and may thus be important for their dissemination into the environment. To get an overview of their occurrence and characteristics, we investigated process water (n = 50) from delivery and unclean areas as well as wastewater (n = 32) from the in-house wastewater treatment plants (WWTPs) of two German poultry slaughterhouses (slaughterhouses S1 and S2). The samples were screened for ESKAPE bacteria (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) and Escherichia coli Their antimicrobial resistance phenotypes and the presence of extended-spectrum-β-lactamase (ESBL), carbapenemase, and mobilizable colistin resistance genes were determined. Selected ESKAPE bacteria were epidemiologically classified using different molecular typing techniques. At least one of the target species was detected in 87.5% (n = 28/32) of the wastewater samples and 86.0% (n = 43/50) of the process water samples. The vast majority of the recovered isolates (94.9%, n = 448/472) was represented by E. coli (39.4%), the A. calcoaceticus-A. baumannii (ACB) complex (32.4%), S. aureus (12.3%), and K. pneumoniae (10.8%), which were widely distributed in the delivery and unclean areas of the individual slaughterhouses, including their wastewater effluents. Enterobacter spp., Enterococcus spp., and P. aeruginosa were less abundant and made up 5.1% of the isolates. Phenotypic and genotypic analyses revealed that the recovered isolates exhibited diverse resistance phenotypes and β-lactamase genes. In conclusion, wastewater effluents from the investigated poultry slaughterhouses exhibited clinically relevant bacteria (E. coli, methicillin-resistant S. aureus, K. pneumoniae, and species of the ACB and Enterobacter cloacae complexes) that contribute to the dissemination of clinically relevant resistances (i.e., blaCTX-M or blaSHV and mcr-1) in the environment.IMPORTANCE Bacteria from livestock may be opportunistic pathogens and carriers of clinically relevant resistance genes, as many antimicrobials are used in both veterinary and human medicine. They may be released into the environment from wastewater treatment plants (WWTPs), which are influenced by wastewater from slaughterhouses, thereby endangering public health. Moreover, process water that accumulates during the slaughtering of poultry is an important reservoir for livestock-associated multidrug-resistant bacteria and may serve as a vector of transmission to occupationally exposed slaughterhouse employees. Mitigation solutions aimed at the reduction of the bacterial discharge into the production water circuit as well as interventions against their further transmission and dissemination need to be elaborated. Furthermore, the efficacy of in-house WWTPs needs to be questioned. Reliable data on the occurrence and diversity of clinically relevant bacteria within the slaughtering production chain and in the WWTP effluents in Germany will help to assess their impact on public and environmental health.
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Affiliation(s)
- Mykhailo Savin
- Institute of Animal Sciences, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Marijo Parcina
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Esther Sib
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Alexander Voigt
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Judith Kreyenschmidt
- Institute of Animal Sciences, University of Bonn, Bonn, Germany
- Hochschule Geisenheim University, Department of Fresh Produce Logistics, Geisenheim, Germany
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17
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Robé C, Blasse A, Merle R, Friese A, Roesler U, Guenther S. Low Dose Colonization of Broiler Chickens With ESBL-/AmpC- Producing Escherichia coli in a Seeder-Bird Model Independent of Antimicrobial Selection Pressure. Front Microbiol 2019; 10:2124. [PMID: 31572330 PMCID: PMC6753873 DOI: 10.3389/fmicb.2019.02124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/29/2019] [Indexed: 01/05/2023] Open
Abstract
Extended-spectrum beta-lactamase- (ESBL-) and AmpC beta-lactamase- (AmpC-) producing Enterobacteriaceae pose a risk for both human and animal health. For livestock, highest prevalences have been reported in broiler chickens, which are therefore considered as a reservoir of multidrug-resistant bacteria. The possibility of transfer to humans either by a close contact to colonized broiler flocks or through contaminated retail meat results in the necessity to develop intervention measures for the entire broiler production chain. In this regard, a basic understanding of the colonization process is mandatory including the determination of the minimal bacterial load leading to a persistent colonization of broiler chickens. Therefore, we conducted a bivalent broiler colonization study close to real farming conditions without applying any antimicrobial selection pressure. ESBL- and AmpC- negative broiler chickens (Ross 308) were co- colonized on their third day of life with two strains: one CTX-M-15-producing Escherichia coli-ST410 and one CMY-2/mcr-1-positive E. coli-ST10. Colonization was assessed by cloacal swabs over the period of the trial, starting 24 h post inoculation. During the final necropsy, the contents of crop, jejunum, cecum, and colon were quantified for the occurrence of both bacterial strains. To define the minimal oral colonization dosage 104 to 101 colony forming units (cfu) were orally inoculated to four separately housed broiler groups (each n = 19, all animals inoculated) and a dosage of already 101 cfu E. coli led to a persistent colonization of all animals of the group after 3 days. To assure stable colonization, however, a dosage of 102 cfu E. coli was chosen for the subsequent seeder-bird trial. In the seeder-bird trial one fifth of the animals (seeder, n = 4) were orally inoculated and kept together with the non-inoculated animals (sentinel, n = 16) to mimic the route of natural infection. After 35 days of trial, all animals were colonized with both E. coli strains. Given the low colonization dosage and the low seeder/sentinel ratio, the rapid spread of ESBL- and AmpC- producing Enterobacteriaceae in conventional broiler farms currently seems inevitably resulting in an urgent need for the development of intervention strategies to reduce colonization of broilers during production.
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Affiliation(s)
- Caroline Robé
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Anja Blasse
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Roswitha Merle
- Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
| | - Anika Friese
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Guenther
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
- Institute of Pharmacy, Pharmaceutical Biology, Universität Greifswald, Greifswald, Germany
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Emergence of two novel sequence types (3366 and 3367) NDM-1- and OXA-48-co-producing K. pneumoniae in Italy. Eur J Clin Microbiol Infect Dis 2019; 38:1687-1691. [PMID: 31165962 DOI: 10.1007/s10096-019-03597-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 01/26/2023]
Abstract
The aim of this study was to analyze the alarming spread of NDM-1- and OXA-48-co-producing Klebsiella pneumoniae clinical isolates, collected between October 2016 and January 2018 in a neonatal intensive care unit of the University Hospital, Catania, Italy, through whole genome sequencing. All confirmed carbapenem-resistant K. pneumoniae (CRKp) isolates were characterized pheno- and geno-typically, as well as by whole genome sequencing (WGS). A total of 13 CRKp isolates were identified from 13 patients. Pulsed-field gel electrophoresis (PFGE) was performed, and the multilocus sequence typing (MLST) scheme used was based on the gene sequence as published on the MLST Pasteur website. Core genome MLST (cgMLST) was also performed. All isolates co-carried blaoxa-48 and blaNDM-1 genes located on different plasmids belonging to the IncM/L and IncA/C2 groups, respectively. The 13 strains had identical PFGE profiles. MLST and cgMLST showed that K. pneumoniae was dominated by CRKp ST101 and two novel STs (ST3666 and ST3367), identified after submission to the MLST database for ST assignment. All isolates shared the same virulence factors such as type 3 fimbriae, genes for yersiniabactin biosynthesis, yersiniabactin receptor, and iron ABC transporter. They carried the wzi137 variant associated with the K17 serotype. To the best of our knowledge, this is the first report of two novel STs, 3366 and 3367, NDM-OXA-48-co-producing K. pneumoniae clinical isolates, in Italy.
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Ferreira RL, da Silva BCM, Rezende GS, Nakamura-Silva R, Pitondo-Silva A, Campanini EB, Brito MCA, da Silva EML, Freire CCDM, da Cunha AF, Pranchevicius MCDS. High Prevalence of Multidrug-Resistant Klebsiella pneumoniae Harboring Several Virulence and β-Lactamase Encoding Genes in a Brazilian Intensive Care Unit. Front Microbiol 2019; 9:3198. [PMID: 30723463 PMCID: PMC6349766 DOI: 10.3389/fmicb.2018.03198] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 12/10/2018] [Indexed: 01/24/2023] Open
Abstract
Klebsiella pneumoniae is an important opportunistic pathogen that commonly causes nosocomial infections and contributes to substantial morbidity and mortality. We sought to investigate the antibiotic resistance profile, pathogenic potential and the clonal relationships between K. pneumoniae (n = 25) isolated from patients and sources at a tertiary care hospital's intensive care units (ICUs) in the northern region of Brazil. Most of K. pneumoniae isolates (n = 21, 84%) were classified as multidrug resistant (MDR) with high-level resistance to β-lactams, aminoglycosides, quinolones, tigecycline, and colistin. All the 25 isolates presented extended-spectrum beta-lactamase-producing (ESBL), including carbapenemase producers, and carried the bla KPC (100%), bla TEM (100%), bla SHV variants (n = 24, 96%), bla OXA-1 group (n = 21, 84%) and bla CTX-M-1 group (n = 18, 72%) genes. The K2 serotype was found in 4% (n = 1) of the isolates, and the K1 was not detected. The virulence-associated genes found among the 25 isolates were mrkD (n = 24, 96%), fimH-1 (n = 22, 88%), entB (100%), iutA (n = 10, 40%), ybtS (n = 15, 60%). The genes related with efflux pumps and outer membrane porins found were AcrAB (100%), tolC (n = 24, 96%), mdtK (n = 22, 88%), OmpK35 (n = 15, 60%), and OmpK36 (n = 7, 28%). ERIC-PCR was employed to determine the clonal relationship between the different isolated strains. The obtained ERIC-PCR patterns revealed that the similarity between isolates was above 70%. To determine the sequence types (STs) a multilocus sequence typing (MLST) assay was used. The results indicated the presence of high-risk international clones among the isolates. In our study, the wide variety of MDR K. pneumoniae harboring β-lactams and virulence genes strongly suggest a necessity for the implementation of effective strategies to prevent and control the spread of antibiotic resistant infections.
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Affiliation(s)
- Roumayne L. Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Laboratório Central de Saúde Pública do Tocantins, Palmas, Brazil
| | - Brenda C. M. da Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Graziela S. Rezende
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | | | | | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | | | - Eulália M. L. da Silva
- Department of Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | | | - Anderson F. da Cunha
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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