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Mumtaz MN, Irfan M, Siraj S, Khan A, Khan H, Imran M, Khan IA, Khan A. Whole-genome sequencing of extensively drug-resistant Salmonella enterica serovar Typhi clinical isolates from the Peshawar region of Pakistan. J Infect Public Health 2024; 17:271-282. [PMID: 38134602 DOI: 10.1016/j.jiph.2023.12.002] [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: 07/31/2023] [Revised: 09/18/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Typhoid fever, caused by Salmonella enterica serovar Typhi, is a significant public health concern due to the escalating of antimicrobial resistance (AMR), with limited treatment options for extensively drug-resistant (XDR) S. Typhi strains pose a serious threat to disease management and control. This study aimed to investigate the genomic characteristics, epidemiology and AMR genes of XDR S. Typhi strains from typhoid fever patients in Pakistan. METHODOLOGY We assessed 200 patients with enteric fever symptoms, confirming 65 S. Typhi cases through culturing and biochemical tests. Subsequent antimicrobial susceptibility testing revealed 40 cases of extensively drug-resistant (XDR) and 25 cases of multi-drug resistance (MDR). Thirteen XDR strains were selected for whole-genome sequencing, to analyze their sequence type, phylogenetics, resistance genes, pathogenicity islands, and plasmid sequences using variety of data analysis resources. Pangenome analysis was conducted for 140 XDR strains, including thirteen in-house and 127 strains reported from other regions of Pakistan, to assess their genetic diversity and functional annotation. RESULTS MLST analysis classified all isolates as sequence type 1 (ST-1) with 4.3.1.1. P1 genotype characterization. Prophage and Salmonella Pathogenicity Island (SPI) analysis identified intact prophages and eight SPIs involved in Salmonella's invasion and replication within host cells. Genome data analysis revealed numerous AMR genes including dfrA7, sul1, qnrS1, TEM-1, Cat1, and CTX-M-15, and SNPs associated with antibiotics resistance. IncY, IncQ1, pMAC, and pAbTS2 plasmids, conferring antimicrobial resistance, were detected in a few XDR S. Typhi strains. Phylogenetic analysis inferred a close epidemiological linkage among XDR strains from different regions of Pakistan. Pangenome was noted closed among these strains and functional annotation highlighted genes related to metabolism and pathogenesis. CONCLUSION This study revealed a uniform genotypic background among XDR S. Typhi strains in Pakistan, signifying a persistence transmission of a single, highly antibiotic-resistant clone. The closed pan-genome observed underscores limited genetic diversity and highlights the importance of genomic surveillance for combating drug-resistant typhoid infections.
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Affiliation(s)
- Mah Noor Mumtaz
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan
| | - Muhammad Irfan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Sami Siraj
- Institute of Pharmaceutical Sciences, Khyber Medical University (KMU), Peshawar, Pakistan
| | - Aslam Khan
- Department of Pathology, Medical Teaching Institution MTI, Hayatabad Medical Complex (HMC), Peshawar, Pakistan
| | - Hizbullah Khan
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Muhammad Imran
- Research center for Advanced Materials Science (RCAMS), Chemistry Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan.
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Guarneri F, Bertasio C, Romeo C, Formenti N, Scali F, Parisio G, Canziani S, Boifava C, Guadagno F, Boniotti MB, Alborali GL. First Detection of mcr-9 in a Multidrug-Resistant Escherichia coli of Animal Origin in Italy Is Not Related to Colistin Usage on a Pig Farm. Antibiotics (Basel) 2023; 12:antibiotics12040689. [PMID: 37107051 PMCID: PMC10134971 DOI: 10.3390/antibiotics12040689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
The emergence of colistin resistance raises growing concerns because of its use as a last-resort antimicrobial for the treatment of severe gram-negative bacterial infections in humans. Plasmid-borne mobile colistin resistance genes (mcr) are particularly worrisome due to their high propensity to spread. An mcr-9-positive Escherichia coli was isolated from a piglet in Italy, representing the first isolation of this gene from an E. coli of animal origin in the country. Whole genome sequencing (WGS) revealed that mcr-9 was borne by an IncHI2 plasmid carrying several other resistance genes. The strain was indeed phenotypically resistant to six different antimicrobial classes, including 3rd and 4th generation cephalosporins. Despite the presence of mcr-9, the isolate was susceptible to colistin, probably because of a genetic background unfavourable to mcr-9 expression. The lack of colistin resistance, coupled with the fact that the farm of origin had not used colistin in years, suggests that mcr-9 in such a multidrug-resistant strain can be maintained thanks to the co-selection of neighbouring resistance genes, following usage of different antimicrobials. Our findings highlight how a comprehensive approach, integrating phenotypical testing, targeted PCR, WGS-based techniques, and information on antimicrobial usage is crucial to shed light on antimicrobial resistance.
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Affiliation(s)
- Flavia Guarneri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Cristina Bertasio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Claudia Romeo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Nicoletta Formenti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Federico Scali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Giovanni Parisio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Sabrina Canziani
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Chiara Boifava
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Federica Guadagno
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Maria Beatrice Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Giovanni Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
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Freire S, Grilo T, Nordmann P, Poirel L, Aires-de-Sousa M. Multiplex PCR for detection of acquired plasmid-borne fosfomycin resistance fos genes in Escherichia coli. Diagn Microbiol Infect Dis 2023; 105:115864. [PMID: 36502596 DOI: 10.1016/j.diagmicrobio.2022.115864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
A rapid (<3 hours) and reliable multiplex PCR was developed for detecting simultaneously known plasmid-mediated fos genes conferring acquired resistance to fosfomycin. Our technique was tested on a collection of Escherichia coli isolates previously identified as bearing the fosA-, fosC- and fosL-like genes, showing a sensitivity and a specificity of 100%.
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Affiliation(s)
- Samanta Freire
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Teresa Grilo
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Patrice Nordmann
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Marta Aires-de-Sousa
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal; Escola Superior de Saúde da Cruz Vermelha Portuguesa - Lisboa (ESSCVP-Lisboa), Lisboa, Portugal; Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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Mak PHW, Rehman MA, Kiarie EG, Topp E, Diarra MS. Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: a review. J Anim Sci Biotechnol 2022; 13:148. [PMID: 36514172 DOI: 10.1186/s40104-022-00786-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/18/2022] [Indexed: 12/15/2022] Open
Abstract
Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers, despite substantial efforts in prevention and control. Antibiotics have been used not only for the treatment and prevention of such diseases, but also for growth promotion. Consequently, these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans, animals, and the environment. To break down the antimicrobial resistance (AMR), poultry producers are restricting the antimicrobial use (AMU) while adopting the antibiotic-free (ABF) and organic production practices to satisfy consumers' demands. However, it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome. Various Gram-negative (Salmonella enterica serovars, Campylobacter jejuni/coli, E. coli) and Gram-positive (Enterococcus spp., Staphylococcus spp. and C. perfringens) bacteria harboring multiple AMR determinants have been reported in poultry including organically- and ABF-raised chickens. In this review, we discussed major poultry production systems (conventional, ABF and organic) and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportunities to develop efficient and safe production practices in controlling pathogens.
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Affiliation(s)
- Philip H W Mak
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Guelph, ON, Canada.,Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Muhammad Attiq Rehman
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Guelph, ON, Canada
| | - Elijah G Kiarie
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Edward Topp
- London Research and Development Center, AAFC, London, ON, Canada
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Guelph, ON, Canada.
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Ramtahal MA, Amoako DG, Ismail A, Bester L, Abia ALK, Essack SY. Salmonella Yoruba: a rare serotype revealed through genomic sequencing along the farm-to-fork continuum of an intensive poultry farm in KwaZulu-Natal, South Africa. Acta Trop 2022; 234:106620. [PMID: 35907503 DOI: 10.1016/j.actatropica.2022.106620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/08/2022] [Accepted: 07/26/2022] [Indexed: 11/01/2022]
Abstract
Salmonella enterica is a zoonotic pathogen of worldwide public health importance. We characterised Salmonella isolates from poultry along the farm-to-fork continuum using whole genome sequencing (WGS) and bioinformatics analysis. Three multilocus sequence types (MLSTs), i.e., ST15 (1.9%), ST152 (5.9%) and ST1316 (92.2%) and three serotypes, i.e., S. Heidelberg (1.9%), Kentucky (5.9%) and Yoruba (92.2%) were detected. The rare serotype, S. Yoruba, was detected among the farm and abattoir isolates and contained resistance and virulence determinants. Resistome analysis revealed the presence of the aac(6')-Iaa gene associated with aminoglycoside resistance, a single point mutation in the parC gene associated with fluoroquinolone and quinolone resistance, and a single isolate contained the fosA7 gene responsible for fosfomycin resistance. No antibiotic resistance genes (ARGs) were identified for isolates phenotypically non-susceptible to azithromycin, cephalosporins, chloramphenicol and nitrofurantoin and resistance was thought to be attributable to other resistance mechanisms. The fully susceptible profiles observed for the wastewater isolates suggest that the poultry environment may receive antibiotic-resistant strains and resistance determinants from poultry with the potential of becoming a pathway of Salmonella transmission along the continuum. Six plasmids were identified and were only carried by 92.2% of the S. Yoruba isolates in varying combinations. Four plasmids were common to all S. Yoruba isolates along the continuum; isolates from the litter and faeces on the farm contained two additional plasmids. Ten Salmonella pathogenicity islands (SPIs) and 177 virulence genes were identified; some were serotype-specific. Phylogenetic analysis of S. Heidelberg and Kentucky showed that isolates were related to animal and human isolates from other countries. Phylogenetic analysis among the S. Yoruba isolates revealed four clades based on the isolate sources along the farm-to-fork continuum. Although the transmission of Salmonella strains along the farm-to-fork continuum was not evident, pathogenic, resistant Salmonella present in the poultry production chain poses a food safety risk. WGS analysis can provide important information on the spread, resistance, pathogenicity, and epidemiology of isolates and new, rare or emerging Salmonella strains to develop intervention strategies to improve food safety.
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Affiliation(s)
- Melissa A Ramtahal
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Arshad Ismail
- Core Sequencing Facility, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Linda Bester
- Biomedical Research Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Akebe L K Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; Environmental Research Foundation, Westville 3630, KwaZulu-Natal
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
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Spread and Molecular Characteristics of
Enterobacteriaceae
Carrying
fosA
-Like Genes from Farms in China. Microbiol Spectr 2022; 10:e0054522. [PMID: 35852324 PMCID: PMC9431306 DOI: 10.1128/spectrum.00545-22] [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] [Indexed: 11/20/2022] Open
Abstract
Here, we report the widespread and complex genetic environments of
fosA
-like genes in animal-derived strains in China. The
fosA7.5
gene was identified in this study and was found to confer resistance to fosfomycin.
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7
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Extended-Spectrum-β-Lactamase- and AmpC-Producing Escherichia coli in Domestic Dogs: Spread, Characterisation and Associated Risk Factors. Antibiotics (Basel) 2021; 10:antibiotics10101251. [PMID: 34680831 PMCID: PMC8533012 DOI: 10.3390/antibiotics10101251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/07/2021] [Accepted: 10/14/2021] [Indexed: 01/18/2023] Open
Abstract
In veterinary medicine, the issue of antimicrobial resistance was mainly addressed in food-producing animals (although companion animals also deserve attention). Indeed, these species may be reservoir of resistant microorganisms, such as extended-spectrum β-lactamase and AmpC (ESBL/AmpC)-producing bacteria. Dogs in particular may transmit them to close-contact humans. Overall 266 faecal samples of healthy dogs were microbiologically and molecularly analyzed to investigate ESBL/AmpC-producing Escherichia coli and the effects of host and environmental factors on their spread. A prevalence of 25.9% of ESBL/AmpC-producing E. coli, supported by blaCTX-M (79.7%), blaTEM (47.8%), blaCMY (13%), and blaSHV (5.8%) gene detection, emerged. Dogs frequenting extra-urban environments showed significantly higher odds of being positive to ESBL/AmpC E. coli (30.2%) compared to urban dogs (16.7%) identifying the environment as a risk factor. About 88.4% of isolates were resistant to cephalosporins, 8.7% to cephalosporins and carbapenems, and 2.9% to cephalosporins, carbapenems, and penicillins. ESBL/AmpC-producing E. coli expressing blaCMY were significantly more resistant to cefoxitin, cefotaxime/clavulanic acid and ceftazidime/clavulanic acid, highlighting its negative effects. Our results suggest the role of domestic dogs as a maintenance host of ESBL/AmpC-producing E. coli leading to a constant health monitoring. The recorded resistances to carbapenems implies attention and further investigations.
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Melo RT, Galvão NN, Guidotti-Takeuchi M, Peres PABM, Fonseca BB, Profeta R, Azevedo VAC, Monteiro GP, Brenig B, Rossi DA. Molecular Characterization and Survive Abilities of Salmonella Heidelberg Strains of Poultry Origin in Brazil. Front Microbiol 2021; 12:674147. [PMID: 34220757 PMCID: PMC8253257 DOI: 10.3389/fmicb.2021.674147] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/12/2021] [Indexed: 12/02/2022] Open
Abstract
The aim of the study was to evaluate the genotypic and phenotypic characteristics of 20 strains of S. Heidelberg (SH) isolated from broilers produced in southern Brazil. The similarity and presence of genetic determinants linked to virulence, antimicrobial resistance, biofilm formation, and in silico-predicted metabolic interactions revealed this serovar as a threat to public health. The presence of the ompC, invA, sodC, avrA, lpfA, and agfA genes was detected in 100% of the strains and the luxS gene in 70% of them. None of the strains carries the blaSHV, mcr-1, qnrA, qnrB, and qnrS genes. All strains showed a multidrug-resistant profile to at least three non-β-lactam drugs, which include colistin, sulfamethoxazole, and tetracycline. Resistance to penicillin, ceftriaxone (90%), meropenem (25%), and cefoxitin (25%) were associated with the presence of blaCTX–M and blaCMY–2 genes. Biofilm formation reached a mature stage at 25 and 37°C, especially with chicken juice (CJ) addition. The sodium hypochlorite 1% was the least efficient in controlling the sessile cells. Genomic analysis of two strains identified more than 100 virulence genes and the presence of resistance to 24 classes of antibiotics correlated to phenotypic tests. Protein-protein interaction (PPI) prediction shows two metabolic pathways correlation with biofilm formation. Virulence, resistance, and biofilm determinants must be constant monitoring in SH, due to the possibility of occurring infections extremely difficult to cure and due risk of the maintenance of the bacterium in production environments.
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Affiliation(s)
- Roberta T Melo
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Newton N Galvão
- Ministry of Agriculture, Livestock and Supply, Rio de Janeiro, Brazil
| | | | - Phelipe A B M Peres
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Belchiolina B Fonseca
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme P Monteiro
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Daise A Rossi
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
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Comparison of Antimicrobial Resistance Detected in Environmental and Clinical Isolates from Historical Data for the US. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4254530. [PMID: 32351993 PMCID: PMC7174961 DOI: 10.1155/2020/4254530] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/12/2020] [Accepted: 02/22/2020] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance (AMR) has become an urgent public health issue, as pathogens are becoming increasingly resistant to commonly used antimicrobials. While AMR isolate data are available in the NCBI Pathogen Detection Isolates Browser (NPDIB) database, few researches have been performed to compare antimicrobial resistance detected in environmental and clinical isolates. To address this, this work conducted the first multivariate statistical analysis of antimicrobial-resistance pathogens detected in NPDIB clinical and environmental isolates for the US from 2013 to 2018. The highly occurring AMR genes and pathogens were identified for both clinical and environmental settings, and the historical profiles of those genes and pathogens were then compared for the two settings. It was found that Salmonella enterica and E. coli and Shigella were the highly occurring AMR pathogens for both settings. Additionally, the genes fosA, oqxB, ble, floR, fosA7, mcr-9.1, aadA1, aadA2, ant(2")-Ia, aph(3")-Ib, aph(3')-Ia, aph(6)-Id, blaTEM-1, qacEdelta1, sul1, sul2, tet(A), and tet(B) were mostly detected for both clinical and environmental settings. Ampicillin, ceftriaxone, gentamicin, tetracycline, and cefoxitin were the antimicrobials which got the most resistance in both settings. The historical profiles of these genes, pathogens, and antimicrobials indicated that higher occurrence frequencies generally took place earlier in the environmental setting than in the clinical setting.
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