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Qiu Y, Xu H, Huang M, Chen J, Yang J, Weng S. Phenotypic and genomic characterization of a multidrug-resistant Salmonella enterica serovar Kentucky ST198 isolated from a patient in China. J Glob Antimicrob Resist 2024; 38:106-110. [PMID: 38723710 DOI: 10.1016/j.jgar.2024.04.003] [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: 08/01/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 06/29/2024] Open
Abstract
OBJECTIVES The objective of this study was to investigate the resistance mechanisms of a multidrug-resistant Salmonella Kentucky ST198 FJ-2064 isolated from a patient in China. METHODS The antimicrobial susceptibility of FJ-2064 was determined by the standard disc dilution and broth microdilution methods. The complete genome of FJ-2064 was sequenced using PacBio and Illumina MiSeq platforms. Polymerase chain reaction (PCR) and S1-PFGE were utilized to confirm the mutation sites and the genomic plasmids, respectively. RESULTS Isolate FJ-2064 belongs to sequence type ST198 and harboured no visible large plasmids, but was concurrent resistant to 22 detected antimicrobial agents including cefotaxime, ciprofloxacin, and azithromycin. The complete genome sequence identified 20 acquired antibiotic resistance genes (ARGs) and five chromosomal mutations in the gyrA and parC genes of the quinolone resistance determining regions (QRDRs) in FJ-2064. In addition, PCR sequencing confirmed that most of the ARGs were clustered on one multidrug-resistant region and a variant of SGI1-K. In particular, the bla-TEM-1 and bla-CTX-M-55, qnrS1, mph(A) genes, which confer resistance to cephalosporins, quinolones, and macrolides respectively, were all located on the multidrug-resistant region. CONCLUSIONS We have demonstrated one multidrug-resistant region and a variant of SGI1-K in a Salmonella Kentucky ST198 that is co-resistant to cefotaxime, ciprofloxacin, and azithromycin.
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Affiliation(s)
- Yufeng Qiu
- Fujian Provincial Center for Disease Control and Prevention, Fuzhou 350011, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350011, China; Fujian Institute of Preventive Medicine, Fuzhou, 350012, China
| | - Haibin Xu
- Fujian Provincial Center for Disease Control and Prevention, Fuzhou 350011, China; Fujian Institute of Preventive Medicine, Fuzhou, 350012, China
| | - Mengying Huang
- Fujian Provincial Center for Disease Control and Prevention, Fuzhou 350011, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350011, China
| | - Jianhui Chen
- Fujian Provincial Center for Disease Control and Prevention, Fuzhou 350011, China
| | - Jinsong Yang
- Fujian Provincial Center for Disease Control and Prevention, Fuzhou 350011, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350011, China; Fujian Institute of Preventive Medicine, Fuzhou, 350012, China
| | - Shuntai Weng
- Fujian Provincial Center for Disease Control and Prevention, Fuzhou 350011, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350011, China; Fujian Institute of Preventive Medicine, Fuzhou, 350012, China.
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Bhattacharjee A, Singh AK. Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil. J Microbiol 2024; 62:511-523. [PMID: 38904697 DOI: 10.1007/s12275-024-00129-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/25/2024] [Accepted: 02/22/2024] [Indexed: 06/22/2024]
Abstract
Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing & analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.
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Affiliation(s)
- Abhilash Bhattacharjee
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India
- Department of Botany, Dibrugarh Hanumanbax Surajmall Kanoi College, Dibrugarh, 786001, Assam, India
| | - Anil Kumar Singh
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India.
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Intuy R, Supa-Amornkul S, Jaemsai B, Ruangchai W, Wiriyarat W, Chaturongakul S, Palittapongarnpim P. A novel variant in Salmonella genomic island 1 of multidrug-resistant Salmonella enterica serovar Kentucky ST198. Microbiol Spectr 2024; 12:e0399423. [PMID: 38687075 PMCID: PMC11237444 DOI: 10.1128/spectrum.03994-23] [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: 11/20/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
Salmonella enterica serovar Kentucky ST198 is a major health threat due to its resistance to ciprofloxacin and several other drugs, including third-generation cephalosporins. Many drug-resistant genes have been identified in the Salmonella genomic island 1 variant K (SGI1-K). In this study, we investigated the antimicrobial resistance (AMR) profile and genotypic relatedness of two isolates of ciprofloxacin-resistant (CIPR) S. Kentucky ST198 from poultry in Northeastern Thailand. We successfully assembled the complete genomes of both isolates, namely SSSE-01 and SSSE-03, using hybrid de novo assembly of both short- and long-read sequence data. The complete genomes revealed their highly similar genomic structures and a novel variant of SGI1-K underlying multidrug-resistant (MDR) patterns, including the presence of blaTEM-1b, which confers resistance to beta-lactams, including cephalosporins and lnu(F) which confers resistance to lincomycin and other lincosamides. In addition, the chromosomal mutations in the quinolone resistance-determining region (QRDR) were found at positions 83 (Ser83Phe) and 87 (Asp87Asn) of GyrA and at positions 57 (Thr57Ser) and 80 (Ser80Ile) of ParC suggesting high resistance to ciprofloxacin. We also compared SSSE-01 and SSSE-03 with publicly available complete genome data and revealed significant variations in SGI1-K genetic structures and variable relationships to antibiotic resistance. In comparison to the other isolates, SGI1-K of SSSE-01 and SSSE-03 had a relatively large deletion in the backbone, spanning from S011 (traG∆) to S027 (resG), and the inversion of the IS26-S044∆-yidY segment. Their MDR region was characterized by the inversion of a large segment, including the mer operon and the relocation of IntI1 and several resistance genes downstream of the IS26-S044∆-yidY segment. These structural changes were likely mediated by the recombination of IS26. The findings broaden our understanding of the possible evolution pathway of SGI1-K in fostering drug resistance, which may provide opportunities to control these MDR strains.IMPORTANCEThe emergence of ciprofloxacin-resistant (CIPR) Salmonella Kentucky ST198 globally has raised significant concerns. This study focuses on two poultry isolates from Thailand, revealing a distinct Salmonella genomic island 1 variant K (SGI1-K) genetic structure. Remarkably, multiple antibiotic resistance genes (ARGs) were identified within the SGI1-K as well as other locations in the chromosome, but not in plasmids. Comparing the SGI1-K genetic structures among global and even within-country isolates unveiled substantial variations. Intriguingly, certain isolates lacked ARGs within the SGI1-K, while others had ARGs relocated outside. The presence of chromosomal extended-spectrum β-lactamase (ESBL) genes and lincosamide resistance, lnu(F), gene, could potentially inform the choices of the treatment of CIPRS. Kentucky ST198 infections in humans. This study highlights the importance of understanding the diverse genetic structures of SGI1-K and emphasizes the role of animals and humans in the emergence of antimicrobial resistance.
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Affiliation(s)
- Rattanaporn Intuy
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sirirak Supa-Amornkul
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Bharkbhoom Jaemsai
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Wuthiwat Ruangchai
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Witthawat Wiriyarat
- Department of Pre-Clinical and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Bangkok, Thailand
| | - Soraya Chaturongakul
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Molecular Medical Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Bangkok, Thailand
| | - Prasit Palittapongarnpim
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
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Berman TS, Barnett-Itzhaki Z, Berman T, Marom E. Antimicrobial resistance in food-producing animals: towards implementing a one health based national action plan in Israel. Isr J Health Policy Res 2023; 12:18. [PMID: 37101188 PMCID: PMC10132406 DOI: 10.1186/s13584-023-00562-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 04/01/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Development of antimicrobial resistance poses a major threat to human and animal health worldwide. Antimicrobials are frequently used in animal husbandry, making food-producing animals a widespread and important source of antimicrobial resistance. Indeed, recent evidence demonstrates that antimicrobial resistance in food-producing animals poses a threat to the health of humans, animals and the environment. To address this threat, national action plans have been implemented based on a 'One Health' approach, which integrates actions across human and animal health sectors to combat antimicrobial resistance. Although under development, Israel has yet to publish a national action plan against antimicrobial resistance, despite alarming findings of resistant bacteria in food-producing animals in the country. Here we review several national action plans against antimicrobial resistance around the world in order to suggest approaches to develop a national action plan in Israel. MAIN BODY We investigated worldwide national action plans against antimicrobial resistance based on a 'One Health' approach. We also conducted interviews with representatives of relevant Israeli ministries to understand antimicrobial resistance policy and regulatory frameworks in Israel. Finally, we present recommendations for Israel towards implementing a 'One Health' national action plan against antimicrobial resistance. Many countries have developed such plans, however, only a few are currently funded. Furthermore, many countries, especially in Europe, have taken action to reduce the use of antimicrobials and the spread of antimicrobial resistance in food-producing animals by banning the use of antimicrobials to promote growth, reporting data on the use and sales of antimicrobials in food-producing animals, operating centralized antimicrobial resistance surveillance systems and preventing the use of antimicrobials important to human medicine to treat food-producing animals. CONCLUSIONS Without a comprehensive and funded national action plan, the risks of antimicrobial resistance to the public health in Israel will escalate. Thus, several actions should be considered: (1) Reporting data on the use of antimicrobials in humans and animals. (2) Operating a centralized surveillance system for antimicrobial resistance in humans, animals and the environment. (3) Improving awareness regarding antimicrobial resistance in the general public and in health practitioners from both human and animal sectors. (4) Composing a list of critically important antimicrobials to human medicine that's use should be avoided in food-producing animals. (5) Enforcing best practices of antimicrobial use at the farm-level. (6) Reducing incidence of infection through farm biosecurity. (7) Supporting research and development of new antimicrobial treatments, vaccines and diagnostic tools.
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Affiliation(s)
- Tali Sarah Berman
- Mimshak, The Israel Society of Ecology and Environmental Sciences, 19 Kehilat New York St, Tel Aviv, Israel.
- Public Health Services, Ministry of Health, 39 Yirmiyahu St, Jerusalem, Israel.
- Department of Entomology, Newe Ya'ar Research Center, ARO, Ramat Yishai, Israel.
| | - Zohar Barnett-Itzhaki
- Ruppin Research Group in Environmental and Social Sustainability, Ruppin Academic Center, 4025000, Emek Hefer, Israel
| | - Tamar Berman
- Public Health Services, Ministry of Health, 39 Yirmiyahu St, Jerusalem, Israel
| | - Eli Marom
- Public Health Services, Ministry of Health, 39 Yirmiyahu St, Jerusalem, Israel
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Bassal R, Davidovich-Cohen M, Yakunin E, Rokney A, Ken-Dror S, Strauss M, Wolf T, Sagi O, Amit S, Moran-Gilad J, Treygerman O, Karyo R, Keinan-Boker L, Cohen D. Trends in the Epidemiology of Non-Typhoidal Salmonellosis in Israel between 2010 and 2021. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20095626. [PMID: 37174146 PMCID: PMC10178198 DOI: 10.3390/ijerph20095626] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Non-typhoidal salmonellosis (NTS) is one of the most common foodborne diseases worldwide. In this study, we aimed to analyze trends in the epidemiology of NTS in the last decade in Israel. Laboratory-confirmed cases of NTS at eight sentinel laboratories were reported to the Israel Sentinel Laboratory-Based Surveillance Network, integrated with the serotype identification performed at the Salmonella National Reference Laboratory of the Ministry of Health. The decrease in NTS incidence since 1999 continued between 2010 and 2014 (16.1 per 100,000 in 2014) and was interrupted by a rise between 2015 and 2017 (39.1 per 100,000 in 2017) associated with outbreaks of Salmonella Enteritidis. The incidence of NTS dropped again thereafter (21.4 per 100,000 in 2021). The 0-4 age group was the most affected by NTS (55.5% of the cases) throughout the surveillance period. The age-adjusted incidence rates were consistently high in the summer months (June-September) and low in the winter months (December-February). The overall decrease in the incidence of NTS in Israel since 1999 was temporarily interrupted in the last decade by country-wide outbreaks involving emerging or re-emerging Salmonella serotypes. Control measures should be enhanced for all risk points of food chain transmission of Salmonella spp. to further reduce the NTS morbidity in Israel.
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Affiliation(s)
- Ravit Bassal
- Israel Center for Disease Control, Ministry of Health, Sheba Medical Center, Ramat Gan 52621, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Maya Davidovich-Cohen
- Salmonella National Reference Center, Public Health Laboratories-Jerusalem (PHL-J) Public Health Services, Ministry of Health, Jerusalmem 34410, Israel
| | - Eugenia Yakunin
- Salmonella National Reference Center, Public Health Laboratories-Jerusalem (PHL-J) Public Health Services, Ministry of Health, Jerusalmem 34410, Israel
| | - Assaf Rokney
- Salmonella National Reference Center, Public Health Laboratories-Jerusalem (PHL-J) Public Health Services, Ministry of Health, Jerusalmem 34410, Israel
| | - Shifra Ken-Dror
- Microbiology Laboratory, Haifa and Western Gallilee, Clalit Health Services, Nesher 36888, Israel
| | - Merav Strauss
- Microbiology Laboratory, Emek Medical Center, Afula 18341, Israel
| | - Tamar Wolf
- Central Laboratory, Maccabi Health Services, Rehovot 76703, Israel
| | - Orli Sagi
- Clinical Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva 84105, Israel
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sharon Amit
- Microbiology Laboratories, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Jacob Moran-Gilad
- Clinical Microbiology Laboratory, The Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem 91120, Israel
| | - Orit Treygerman
- Central Laboratory, Meuhedet Health Services, Lod 71293, Israel
| | - Racheli Karyo
- Central Laboratory, Clalit Health Services, Tel Aviv 61581, Israel
| | - Lital Keinan-Boker
- Israel Center for Disease Control, Ministry of Health, Sheba Medical Center, Ramat Gan 52621, Israel
- School of Public Health, University of Haifa, Haifa 34988, Israel
| | - Dani Cohen
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Srednik ME, Morningstar-Shaw BR, Hicks JA, Mackie TA, Schlater LK. Antimicrobial resistance and genomic characterization of Salmonella enterica serovar Senftenberg isolates in production animals from the United States. Front Microbiol 2022; 13:979790. [PMID: 36406424 PMCID: PMC9668867 DOI: 10.3389/fmicb.2022.979790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/02/2022] [Indexed: 07/22/2023] Open
Abstract
In the USA, Salmonella enterica subspecies enterica serovar Senftenberg is among the top five serovars isolated from food and the top 11 serovars isolated from clinically ill animals. Human infections are associated with exposure to farm environments or contaminated food. The objective of this study was to characterize S. Senftenberg isolates from production animals by analyzing phenotypic antimicrobial resistance profiles, genomic features and phylogeny. Salmonella Senftenberg isolates (n = 94) from 20 US states were selected from NVSL submissions (2014-2017), tested against 14 antimicrobial drugs, and resistance phenotypes determined. Resistance genotypes were determined using whole genome sequencing analysis with AMRFinder and the NCBI and ResFinder databases with ABRicate. Plasmids were detected using PlasmidFinder. Integrons were detected using IntFinder and manual alignment with reference genes. Multilocus-sequence-typing (MLST) was determined using ABRicate with PubMLST database, and phylogeny was determined using vSNP. Among 94 isolates, 60.6% were resistant to at least one antimicrobial and 39.4% showed multidrug resistance. The most prevalent resistance findings were for streptomycin (44.7%), tetracycline (42.6%), ampicillin (36.2%) and sulfisoxazole (32.9%). The most commonly found antimicrobial resistance genes were aac(6')-Iaa (100%), aph(3″)-Ib and aph(6)-Id (29.8%) for aminoglycosides, followed by bla TEM-1 (26.6%) for penicillins, sul1 (25.5%) and sul2 (23.4%) for sulfonamides and tetA (23.4%) for tetracyclines. Quinolone-resistant isolates presented mutations in gyrA and/or parC genes. Class 1 integrons were found in 37 isolates. Thirty-six plasmid types were identified among 77.7% of the isolates. Phylogenetic analysis identified two distinct lineages of S. Senftenberg that correlated with the MLST results. Isolates were classified into two distinct sequence types (ST): ST14 (97.9%) and ST 185 (2.1%). The diversity of this serotype suggests multiple introductions into animal populations from outside sources. This study provided antimicrobial susceptibility and genomic characteristics of S. Senftenberg clinical isolates from production animals in the USA during 2014 to 2017. This study will serve as a base for future studies focused on the phenotypic and molecular antimicrobial characterization of S. Senftenberg isolates in animals. Monitoring of antimicrobial resistance to detect emergence of multidrug-resistant strains is critical.
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Chen CY, Nguyen LHT, Strobaugh TP. Sequence analysis and plasmid mobilization of a 6.6-kb kanamycin resistance plasmid, pSNC3-Kan, from a Salmonella enterica serotype Newport isolate. PLoS One 2022; 17:e0268502. [PMID: 35834529 PMCID: PMC9282650 DOI: 10.1371/journal.pone.0268502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 05/03/2022] [Indexed: 11/19/2022] Open
Abstract
Research on the transfer of antibiotic resistance plasmids has been mainly focused on the large multi-drug resistance conjugative plasmids, while the transmission of small mobilizable plasmids remains under-investigated. A series of diverse ColE-like kanamycin resistance plasmids (“KanR plasmids”) from Salmonella enterica were characterized previously. In this study, the 6.6-kb pSNC3-Kan from a Salmonella enterica serotype Newport isolate was investigated. It possessed highly conserved RNA I/II and Tn602 (IS903-aph-IS903) regions to two other KanR plasmids pSe-Kan and pSBardo-Kan, but carried a mobC-mobA/BD operon. The mobilization proteins encoded by the mob operon of pSNC3-Kan showed high sequence identity (~95%) to those of an E. coli plasmid pEC34B, except that MobE was not present; and were much less conserved to those of another KanR plasmid pSN11/00Kan (43% - 86% identity). Four structurally different KanR plasmids were investigated for their ability to be mobilized by the conjugal transfer (tra) genes from F and IncP plasmids. Transfer genes derived from IncP plasmids can efficiently mobilize KanR plasmids possessing the mob operons (mobC-mobA/BD), such as pSNC3-Kan and pSN11/00Kan, in bi-parental mating experiments. On the other hand, F tra genes were able to mobilize pU302S, pSNC3-Kan and pSe-Kan, but not pSN11/00Kan. A plasmid-borne mob operon was not required for mobilization of the oriT(F)-bearing pSe-Kan by the F tra genes. This study underscores the complexity of plasmid interaction and the importance of how small mobilizable plasmids may contribute to the spread of antibiotic resistance genes.
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Affiliation(s)
- Chin-Yi Chen
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
- * E-mail:
| | - Ly-Huong T. Nguyen
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Terence P. Strobaugh
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
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Cohen E, Kriger O, Amit S, Davidovich M, Rahav G, Gal-Mor O. The emergence of a multidrug resistant Salmonella Muenchen in Israel is associated with horizontal acquisition of the epidemic pESI plasmid. Clin Microbiol Infect 2022; 28:1499.e7-1499.e14. [PMID: 35654317 DOI: 10.1016/j.cmi.2022.05.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Horizontal acquisition of mobile genetic elements is a powerful evolutionary driving force that can profoundly affect pathogens epidemiology and their interactions with the environment and host. In the last decade, the role of the epidemic megaplasmid, pESI was demonstrated in the global emergence of multi-drug resistant (MDR) Salmonella enterica serovar Infantis strains, but it was unknown if this was a one-time phenomenon, or that pESI can drive the emergence of other pathogens. METHODS Epidemiological, molecular, whole genome sequencing, de-novo assembly, bioinformatics and genetic approaches were used to analyze the emergence of a pESI-positive Salmonella enterica serovar Muenchen strain in Israel. RESULTS Since 2018, we report the emergence and high prevalence of S. Muenchen in Israel, which consisted at 2020, 40% (1055/2671) of all clinical Salmonella isolates. We show that the emergence of S. Muenchen is dominated by a clonal MDR strain, report its complete assembled genome sequence, and demonstrate that in contrast to preemergent strains, it harbors the epidemic megaplasmid, pESI, which can be self-mobilized into E. coli and other Salmonella serovars. Additionally, we identified bioinformatically highly similar genomes of clinical isolates that were recently collected in South Africa, UK and USA. CONCLUSIONS This is a second documented case of a pathogen emergence associated with pESI acquisition. Considering the genetic cargo of pESI that enhances resistance, stress tolerance and virulence, and its ability to conjugate into prevalent Salmonella serovars, we provide further support that pESI facilities the emergence and spreading of new Salmonella strains.
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Affiliation(s)
- Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Or Kriger
- Microbiology Laboratory, Sheba Medical Center
| | - Sharon Amit
- Microbiology Laboratory, Sheba Medical Center
| | - Maya Davidovich
- Public Health Laboratories - Jerusalem, Ministry of Health, Jerusalem, Israel
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel.
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9
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Samper-Cativiela C, Diéguez-Roda B, Trigo da Roza F, Ugarte-Ruiz M, Elnekave E, Lim S, Hernández M, Abad D, Collado S, Sáez JL, de Frutos C, Agüero M, Moreno MÁ, Escudero JA, Álvarez J. Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011-2017). Microb Genom 2022; 8. [PMID: 35259085 PMCID: PMC9176280 DOI: 10.1099/mgen.0.000773] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Salmonella Kentucky is commonly found in poultry and rarely associated with human disease. However, a multidrug-resistant (MDR) S. Kentucky clone [sequence type (ST)198] has been increasingly reported globally in humans and animals. Our aim here was to assess if the recently reported increase of S. Kentucky in poultry in Spain was associated with the ST198 clone and to characterize this MDR clone and its distribution in Spain. Sixty-six isolates retrieved from turkey, laying hen and broiler in 2011–2017 were subjected to whole-genome sequencing to assess their sequence type, genetic relatedness, and presence of antimicrobial resistance genes (ARGs), plasmid replicons and virulence factors. Thirteen strains were further analysed using long-read sequencing technologies to characterize the genetic background associated with ARGs. All isolates belonged to the ST198 clone and were grouped in three clades associated with the presence of a specific point mutation in the gyrA gene, their geographical origin and isolation year. All strains carried between one and 16 ARGs whose presence correlated with the resistance phenotype to between two and eight antimicrobials. The ARGs were located in the Salmonella genomic island (SGI-1) and in some cases (blaSHV-12, catA1, cmlA1, dfrA and multiple aminoglycoside-resistance genes) in IncHI2/IncI1 plasmids, some of which were consistently detected in different years/farms in certain regions, suggesting they could persist over time. Our results indicate that the MDR S. Kentucky ST198 is present in all investigated poultry hosts in Spain, and that certain strains also carry additional plasmid-mediated ARGs, thus increasing its potential public health significance.
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Affiliation(s)
- Clara Samper-Cativiela
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain.,Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | | | - Filipa Trigo da Roza
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain.,Molecular Basis of Adaptation, Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, 28040 Madrid, Spain
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain
| | - Ehud Elnekave
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Seunghyun Lim
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55455, USA.,Bioinformatics and Computational Biology Program, University of Minnesota, Rochester, MN 55455, 55455 Minnesota, USA
| | - Marta Hernández
- Molecular Biology and Microbiology Laboratory, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Junta de Castilla y León, 47009 Valladolid, Spain
| | - David Abad
- Molecular Biology and Microbiology Laboratory, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Junta de Castilla y León, 47009 Valladolid, Spain
| | - Soledad Collado
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Dirección General de la Producción Agraria, Ministerio de Agricultura, Pesca y Alimentación, 28010 Madrid, Spain
| | - José Luis Sáez
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Dirección General de la Producción Agraria, Ministerio de Agricultura, Pesca y Alimentación, 28010 Madrid, Spain
| | - Cristina de Frutos
- Laboratorio Central de Veterinaria, Ministerio de Agricultura, Pesca y Alimentación, 28110 Madrid, Spain
| | - Montserrat Agüero
- Laboratorio Central de Veterinaria, Ministerio de Agricultura, Pesca y Alimentación, 28110 Madrid, Spain
| | - Miguel Ángel Moreno
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - José Antonio Escudero
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain.,Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain.,Molecular Basis of Adaptation, Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, 28040 Madrid, Spain
| | - Julio Álvarez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040 Madrid, Spain.,Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
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10
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Nichols M, Gollarza L, Sockett D, Aulik N, Patton E, Watkins LKF, Gambino-Shirley KJ, Folster JP, Chen JC, Tagg KA, Stapleton GS, Trees E, Ellison Z, Lombard J, Morningstar-Shaw B, Schlater L, Elbadawi L, Klos R. Outbreak of Multidrug-Resistant Salmonella Heidelberg Infections Linked to Dairy Calf Exposure, United States, 2015-2018. Foodborne Pathog Dis 2022; 19:199-208. [PMID: 34989634 PMCID: PMC9524362 DOI: 10.1089/fpd.2021.0077] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In August 2016, the Wisconsin Department of Health Services notified the U.S. Centers for Disease Control and Prevention of multidrug-resistant (MDR) Salmonella enterica serovar Heidelberg infections in people who reported contact with dairy calves. Federal and state partners investigated this to identify the source and scope of the outbreak and to prevent further illnesses. Cases were defined as human Salmonella Heidelberg infection caused by a strain that had one of seven pulsed-field gel electrophoresis (PFGE) patterns or was related by whole genome sequencing (WGS), with illness onset from January 1, 2015, through July 2, 2018. Patient exposure and calf purchase information was collected and analyzed; calves were traced back from the point of purchase. Isolates obtained from animal and environmental samples collected on-farm were supplied by veterinary diagnostic laboratories and compared with patient isolates using PFGE and WGS. Antimicrobial susceptibility testing by standardized broth microdilution was performed. Sixty-eight patients from 17 states were identified. Forty (63%) of 64 patients noted cattle contact before illness. Thirteen (33%) of 40 patients with exposure to calves reported that calves were sick or had died. Seven individuals purchased calves from a single Wisconsin livestock market. One hundred forty cattle from 14 states were infected with the outbreak strain. WGS indicated that human, cattle, and environmental isolates from the livestock market were genetically closely related. Most isolates (88%) had resistance or reduced susceptibility to antibiotics of ≥5 antibiotic classes. This resistance profile included first-line antibiotic treatments for patients with severe salmonellosis, including ampicillin, ceftriaxone, and ciprofloxacin. In this outbreak, MDR Salmonella Heidelberg likely spread from sick calves to humans, emphasizing the importance of illness surveillance in animal populations to prevent future spillover of this zoonotic disease.
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Affiliation(s)
- Megin Nichols
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren Gollarza
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Donald Sockett
- Wisconsin Veterinary Diagnostic Laboratory, Madison, Wisconsin, USA
| | - Nicole Aulik
- Wisconsin Veterinary Diagnostic Laboratory, Madison, Wisconsin, USA
| | - Elisabeth Patton
- Wisconsin Department of Agriculture, Trade and Consumer Protection, Madison, Wisconsin, USA
| | - Louise K. Francois Watkins
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kelly J. Gambino-Shirley
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jason P. Folster
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica C. Chen
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kaitlin A. Tagg
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Weems Design Studio, Inc., Suwanee, Georgia, USA
| | - Gregory Sean Stapleton
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Eija Trees
- Association of Public Health Laboratories, Silver Spring, Maryland, USA
| | - Zachary Ellison
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jason Lombard
- Animal and Plant Health Inspection Service, Veterinary Services, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Brenda Morningstar-Shaw
- Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Linda Schlater
- Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Lina Elbadawi
- Wisconsin Department of Health Services, Madison, Wisconsin, USA
| | - Rachel Klos
- Wisconsin Department of Health Services, Madison, Wisconsin, USA
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11
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Srednik ME, Lantz K, Hicks JA, Morningstar-Shaw BR, Mackie TA, Schlater LK. Antimicrobial resistance and genomic characterization of Salmonella Dublin isolates in cattle from the United States. PLoS One 2021; 16:e0249617. [PMID: 34547028 PMCID: PMC8454963 DOI: 10.1371/journal.pone.0249617] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/01/2021] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica subspecies enterica serotype Dublin is a host-adapted serotype in cattle, associated with enteritis and systemic disease. The primary clinical manifestation of Salmonella Dublin infection in cattle, especially calves, is respiratory disease. While rare in humans, it can cause severe illness, including bacteremia, with hospitalization and death. In the United States, S. Dublin has become one of the most multidrug-resistant serotypes. The objective of this study was to characterize S. Dublin isolates from sick cattle by analyzing phenotypic and genotypic antimicrobial resistance (AMR) profiles, the presence of plasmids, and phylogenetic relationships. S. Dublin isolates (n = 140) were selected from submissions to the NVSL for Salmonella serotyping (2014-2017) from 21 states. Isolates were tested for susceptibility against 14 class-representative antimicrobial drugs. Resistance profiles were determined using the ABRicate with Resfinder and NCBI databases, AMRFinder and PointFinder. Plasmids were detected using ABRicate with PlasmidFinder. Phylogeny was determined using vSNP. We found 98% of the isolates were resistant to more than 4 antimicrobials. Only 1 isolate was pan-susceptible and had no predicted AMR genes. All S. Dublin isolates were susceptible to azithromycin and meropenem. They showed 96% resistance to sulfonamides, 97% to tetracyclines, 95% to aminoglycosides and 85% to beta-lactams. The most common AMR genes were: sulf2 and tetA (98.6%), aph(6)-Id (97.9%), aph(3'')-Ib, (97.1%), floR (94.3%), and blaCMY-2 (85.7%). All quinolone resistant isolates presented mutations in gyrA. Ten plasmid types were identified among all isolates with IncA/C2, IncX1, and IncFII(S) being the most frequent. The S. Dublin isolates show low genomic genetic diversity. This study provided antimicrobial susceptibility and genomic insight into S. Dublin clinical isolates from cattle in the U.S. Further sequence analysis integrating food and human origin S. Dublin isolates may provide valuable insight on increased virulence observed in humans.
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Affiliation(s)
- Mariela E. Srednik
- United States Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Ames, Iowa, United States of America
- * E-mail:
| | - Kristina Lantz
- United States Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Ames, Iowa, United States of America
| | - Jessica A. Hicks
- United States Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Ames, Iowa, United States of America
| | - Brenda R. Morningstar-Shaw
- United States Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Ames, Iowa, United States of America
| | - Tonya A. Mackie
- United States Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Ames, Iowa, United States of America
| | - Linda K. Schlater
- United States Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, Ames, Iowa, United States of America
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12
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Kuźmińska-Bajor M, Śliwka P, Ugorski M, Korzeniowski P, Skaradzińska A, Kuczkowski M, Narajaczyk M, Wieliczko A, Kolenda R. Genomic and functional characterization of five novel Salmonella-targeting bacteriophages. Virol J 2021; 18:183. [PMID: 34496915 PMCID: PMC8425127 DOI: 10.1186/s12985-021-01655-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/29/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The host-unrestricted, non-typhoidal Salmonella enterica serovar Enteritidis (S. Enteritidis) and the serovar Typhimurium (S. Typhimurium) are major causative agents of food-borne gastroenteritis, and the host-restricted Salmonella enterica serovar Gallinarum (S. Gallinarum) is responsible for fowl typhoid. Increasing drug resistance in Salmonella contributes to the reduction of effective therapeutic and/or preventive options. Bacteriophages appear to be promising antibacterial tools, able to combat infectious diseases caused by a wide range of Salmonella strains belonging to both host-unrestricted and host-restricted Salmonella serovars. METHODS In this study, five novel lytic Salmonella phages, named UPWr_S1-5, were isolated and characterized, including host range determination by plaque formation, morphology visualization with transmission electron microscopy, and establishment of physiological parameters. Moreover, phage genomes were sequenced, annotated and analyzed, and their genomes were compared with reference Salmonella phages by use of average nucleotide identity, phylogeny, dot plot, single nucleotide variation and protein function analysis. RESULTS It was found that UPWr_S1-5 phages belong to the genus Jerseyvirus within the Siphoviridae family. All UPWr_S phages were found to efficiently infect various Salmonella serovars. Host range determination revealed differences in host infection profiles and exhibited ability to infect Salmonella enterica serovars such as Enteritidis, Gallinarum, Senftenberg, Stanley and Chester. The lytic life cycle of UPWr_S phages was confirmed using the mitomycin C test assay. Genomic analysis revealed that genomes of UPWr_S phages are composed of 51 core and 19 accessory genes, with 33 of all predicted genes having assigned functions. UPWr_S genome organization comparison revealed 3 kinds of genomes and mosaic structure. UPWr_S phages showed very high sequence similarity to each other, with more than 95% average nucleotide identity. CONCLUSIONS Five novel UPWr_S1-5 bacteriophages were isolated and characterized. They exhibit host lysis range within 5 different serovars and are efficient in lysis of both host-unrestricted and host-restricted Salmonella serovars. Therefore, because of their ability to infect various Salmonella serovars and lytic life cycle, UPWr_S1-5 phages can be considered as useful tools in biological control of salmonellosis.
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Affiliation(s)
- Marta Kuźmińska-Bajor
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland.
| | - Paulina Śliwka
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Maciej Ugorski
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Paweł Korzeniowski
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Aneta Skaradzińska
- Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Maciej Kuczkowski
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Magdalena Narajaczyk
- Department of Electron Microscopy, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Alina Wieliczko
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Rafał Kolenda
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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13
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Genomic characterization of an extensively drug-resistant chicken-borne Salmonella Indiana isolate carrying an IncHI2-IncHI2A plasmid. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 2021; 11:12728. [PMID: 34135355 PMCID: PMC8208984 DOI: 10.1038/s41598-021-91456-0] [Citation(s) in RCA: 394] [Impact Index Per Article: 131.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/19/2021] [Indexed: 12/26/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to assessing AMR gene content can be used to detect known resistance mechanisms and potentially identify novel mechanisms. To enable accurate assessment of AMR gene content, as part of a multi-agency collaboration, NCBI developed a comprehensive AMR gene database, the Bacterial Antimicrobial Resistance Reference Gene Database and the AMR gene detection tool AMRFinder. Here, we describe the expansion of the Reference Gene Database, now called the Reference Gene Catalog, to include putative acid, biocide, metal, stress resistance genes, in addition to virulence genes and species-specific point mutations. Genes and point mutations are classified by broad functions, as well as more detailed functions. As we have expanded both the functional repertoire of identified genes and functionality, NCBI released a new version of AMRFinder, known as AMRFinderPlus. This new tool allows users the option to utilize only the core set of AMR elements, or include stress response and virulence genes, too. AMRFinderPlus can detect acquired genes and point mutations in both protein and nucleotide sequence. In addition, the evidence used to identify the gene has been expanded to include whether nucleotide or protein sequence was used, its location in the contig, and presence of an internal stop codon. These database improvements and functional expansions will enable increased precision in identifying AMR genes, linking AMR genotypes and phenotypes, and determining possible relationships between AMR, virulence, and stress response.
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Affiliation(s)
- Michael Feldgarden
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Vyacheslav Brover
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Narjol Gonzalez-Escalona
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, USA
| | - Julie Haendiges
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - James B Pettengill
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Arjun B Prasad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Glenn E Tillman
- Food Safety and Inspection Service, U.S. Department of Agriculture, Athens, GA, USA
| | - Gregory H Tyson
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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15
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Liu Z, Liang Z, Zhou Z, Li L, Meng D, Li X, Tao J, Jiang Z, Gu Y, Huang Y, Liu X, Yang Z, Drewniak L, Liu T, Liu Y, Liu S, Wang J, Jiang C, Yin H. Mobile genetic elements mediate the mixotrophic evolution of novel Alicyclobacillus species for acid mine drainage adaptation. Environ Microbiol 2021; 23:3896-3912. [PMID: 33913568 DOI: 10.1111/1462-2920.15543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 04/12/2021] [Accepted: 04/24/2021] [Indexed: 12/25/2022]
Abstract
Alicyclobacillus species inhabit diverse environments and have adapted to broad ranges of pH and temperature. However, their adaptive evolutions remain elusive, especially regarding the role of mobile genetic elements (MGEs). Here, we characterized the distributions and functions of MGEs in Alicyclobacillus species across five environments, including acid mine drainage (AMD), beverages, hot springs, sediments, and soils. Nine Alicyclobacillus strains were isolated from AMD and possessed larger genome sizes and more genes than those from other environments. Four AMD strains evolved to be mixotrophic and fell into distinctive clusters in phylogenetic tree. Four types of MGEs including genomic island (GI), insertion sequence (IS), prophage, and integrative and conjugative element (ICE) were widely distributed in Alicyclobacillus species. Further, AMD strains did not possess CRISPR-Cas systems, but had more GI, IS, and ICE, as well as more MGE-associated genes involved in the oxidation of iron and sulfide and the resistance of heavy metal and low temperature. These findings highlight the differences in phenotypes and genotypes between strains isolated from AMD and other environments and the important role of MGEs in rapid environment niche expansions.
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Affiliation(s)
- Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zonglin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhicheng Zhou
- College of Plant Protection, Hunan Agricultural University, Changsha, 410010, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
| | - Xiutong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiemeng Tao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yabing Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
| | - Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
| | - Zhendong Yang
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Lukasz Drewniak
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Tianbo Liu
- Hunan Tobacco Science Institute, Changsha, 410010, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, 410010, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
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16
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Montoro-Dasi L, Villagra A, Vega S, Marin C. Influence of farm management on the dynamics of Salmonella enterica serovar Infantis shedding and antibiotic resistance during the growing period of broiler chickens. Vet Rec 2021; 188:e302. [PMID: 33870529 DOI: 10.1002/vetr.302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/26/2020] [Accepted: 03/07/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Salmonella enterica serovar Infantis is a zoonotic pathogen isolated in broilers causing great economic losses in the European poultry sector. It is demonstrated that an investment in management measures at farm level could directly affect the control of food chain microorganisms. The aim of this study was to investigate the development of S. Infantis antimicrobial resistance (AMR) patterns during the growing period, according to flock density and ventilation management, without antibiotic administration. METHODS The experiment was performed in two identical poultry houses, evaluating commercial and optimal farm conditions. At 24 h of rearing, 20% of the animals were orally infected with a S. Infantis strain susceptible to all the antibiotics tested. To study Salmonella shedding, faeces samples from each experimental group were taken weekly and analysed as per ISO/TS 6579-2:2017. Antibiotic susceptibility was assessed according to Decision 2013/653. RESULTS Salmonella shedding showed that the lowest counts were observed in the first week post-infection and highest at slaughter day for both groups. Moreover, 100% of the isolates were multi-resistant. CONCLUSION The acquisition of AMR by S. Infantis starts at the onset of the production cycle and is maintained until the end, demonstrating the importance of transmission of AMR in zoonotic bacteria at farm level.
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Affiliation(s)
- Laura Montoro-Dasi
- Instituto de Ciencia y Tecnología Animal, Universidad Politécnica de Valencia, Valencia, Spain.,Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, Spain
| | - Arantxa Villagra
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, Castellón, Spain
| | - Santiago Vega
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Instituto de Ciencias Biomédicas, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, España
| | - Clara Marin
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Instituto de Ciencias Biomédicas, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, España
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17
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Laure NN, Ahn J. Development of phage-based assay to differentiate ciprofloxacin resistant and sensitive Salmonella Typhimurium. Food Sci Biotechnol 2021; 30:315-320. [PMID: 33732522 DOI: 10.1007/s10068-020-00858-9] [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: 08/24/2020] [Revised: 11/20/2020] [Accepted: 11/27/2020] [Indexed: 10/22/2022] Open
Abstract
This study was designed to evaluate the possibility of using phage-amplification assay for discriminating between antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium. The characteristics of Salmonella phage PBST32 were determined by adsorption rate, one-step growth curve, and lytic activity. The ability of phage-based method to detect S. Typhimurium ATCC 19585 (STCIP) was determined in single culture and bacterial mixtures of S. Typhimurium ATCC 19585 (STWT), Klebsiella pneumoniae, and Staphylococcus aureus. The adsorption rates of PBST32 were 95% and 93% against STWT and STCIP after 20 min, respectively. The PBST32 showed latent period of 20 min and average burst size of 90 against STWT and STCIP. The STCIP was selectively detected in mixtures of S. aureus, K. pneumoniae, and STWT by phage amplification assay. These results provide useful information for designing phage amplification method that can differentially detect antibiotic-resistant pathogens.
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Affiliation(s)
- Nana Nguefang Laure
- Department of Biomedical Science and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
| | - Juhee Ahn
- Department of Biomedical Science and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
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18
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de Curraize C, Siebor E, Neuwirth C. Genomic islands related to Salmonella genomic island 1; integrative mobilisable elements in trmE mobilised in trans by A/C plasmids. Plasmid 2021; 114:102565. [PMID: 33582118 DOI: 10.1016/j.plasmid.2021.102565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/01/2022]
Abstract
Salmonella genomic island 1 (SGI1), an integrative mobilisable element (IME), was first reported 20 years ago, in the multidrug resistant Salmonella Typhimurium DT104 clone. Since this first report, many variants and relatives have been found in Salmonella enterica and Proteus mirabilis. Thanks to whole genome sequencing, more and more complete sequences of SGI1-related elements (SGI1-REs) have been reported in these last few years among Gammaproteobacteria. Here, the genetic organisation and main features common to SGI1-REs are summarised to help to classify them. Their integrases belong to the tyrosine-recombinase family and target the 3'-end of the trmE gene. They share the same genetic organisation (integrase and excisionase genes, replicase module, SgaCD-like transcriptional activator genes, traN, traG, mpsB/mpsA genes) and they harbour AcaCD binding sites promoting their excision, replication and mobilisation in presence of A/C plasmid. SGI1-REs are mosaic structures suggesting that recombination events occurred between them. Most of them harbour a multiple antibiotic resistance (MAR) region and the plasticity of their MAR region show that SGI1-REs play a key role in antibiotic resistance and might help multiple antibiotic resistant bacteria to adapt to their environment. This might explain the emergence of clones with SGI1-REs.
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Affiliation(s)
- Claire de Curraize
- Bacteriology Department, University Hospital Dijon, PBHU, BP 37013, 21070 Dijon Cedex, France; UMR 6249, Chrono-Environnement, PBHU, BP 37013, 21070 Dijon Cedex, France.
| | - Eliane Siebor
- Bacteriology Department, University Hospital Dijon, PBHU, BP 37013, 21070 Dijon Cedex, France; UMR 6249, Chrono-Environnement, PBHU, BP 37013, 21070 Dijon Cedex, France.
| | - Catherine Neuwirth
- Bacteriology Department, University Hospital Dijon, PBHU, BP 37013, 21070 Dijon Cedex, France; UMR 6249, Chrono-Environnement, PBHU, BP 37013, 21070 Dijon Cedex, France.
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Jibril AH, Okeke IN, Dalsgaard A, Menéndez VG, Olsen JE. Genomic Analysis of Antimicrobial Resistance and Resistance Plasmids in Salmonella Serovars from Poultry in Nigeria. Antibiotics (Basel) 2021; 10:99. [PMID: 33498344 PMCID: PMC7909428 DOI: 10.3390/antibiotics10020099] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/06/2021] [Accepted: 01/19/2021] [Indexed: 12/31/2022] Open
Abstract
Antimicrobial resistance is a global public health concern, and resistance genes in Salmonella, especially those located on mobile genetic elements, are part of the problem. This study used phenotypic and genomic methods to identify antimicrobial resistance and resistance genes, as well as the plasmids that bear them, in Salmonella isolates obtained from poultry in Nigeria. Seventy-four isolates were tested for susceptibility to eleven commonly used antimicrobials. Plasmid reconstruction and identification of resistance and virulence genes were performed with a draft genome using in silico approaches in parallel with plasmid extraction. Phenotypic resistance to ciprofloxacin (50.0%), gentamicin (48.6%), nalidixic acid (79.7%), sulphonamides (71.6%) and tetracycline (59.5%) was the most observed. Antibiotic resistance genes (ARGs) detected in genomes corresponded well with these observations. Commonly observed ARGs included sul1, sul2, sul3, tet (A), tet (M), qnrS1, qnrB19 and a variety of aminoglycoside-modifying genes, in addition to point mutations in the gyrA and parC genes. Multiple ARGs were predicted to be located on IncN and IncQ1 plasmids of S. Schwarzengrund and S. Muenster, and most qnrB19 genes were carried by Col (pHAD28) plasmids. Seventy-two percent (19/24) of S. Kentucky strains carried multidrug ARGs located in two distinct variants of Salmonella genomic island I. The majority of strains carried full SPI-1 and SPI-2 islands, suggesting full virulence potential.
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Affiliation(s)
- Abdurrahman Hassan Jibril
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University Sokoto, Sokoto 234840, Nigeria
| | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan 234200, Nigeria;
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
| | - Vanesa García Menéndez
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (A.H.J.); (A.D.); (V.G.M.)
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20
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Dor Z, Shnaiderman-Torban A, Kondratyeva K, Davidovich-Cohen M, Rokney A, Steinman A, Navon-Venezia S. Emergence and Spread of Different ESBL-Producing Salmonella enterica Serovars in Hospitalized Horses Sharing a Highly Transferable IncM2 CTX-M-3-Encoding Plasmid. Front Microbiol 2020; 11:616032. [PMID: 33391248 PMCID: PMC7773750 DOI: 10.3389/fmicb.2020.616032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica is a major causative pathogen of human and animal gastroenteritis. Antibiotic resistant strains have emerged due to the production of extended-spectrum β-lactamases (ESBLs) posing a major health concern. With the increasing reports on ESBL-producing Enterobacterales that colonize companion animals, we aimed to investigate ESBL dissemination among ESBL-producing Salmonella enterica (ESBL-S) in hospitalized horses. We prospectively collected ESBL-S isolates from hospitalized horses in a Veterinary-Teaching Hospital during Dec 2015-Dec 2017. Selection criteria for ESBL-S were white colonies on CHROMagarESBL plates and an ESBL phenotypic confirmation. Salmonella enterica serovars were determined using the Kaufmann-White-Le-Minor serological scheme. ESBL-encoding plasmids were purified, transformed and compared using restriction fragment length polymorphism (RFLP). Whole genome sequencing (Illumina and MinION platforms) were performed for detailed phylogenetic and plasmid analyses. Twelve ESBL-S were included in this study. Molecular investigation and Sequence Read Archive (SRA) meta-analysis revealed the presence of three unique Salmonella enterica serovars, Cerro, Havana and Liverpool, all reported for the first time in horses. PFGE revealed the clonal spread of S. Cerro between seven horses. All twelve isolates carried bla CTX-M- 3 and showed an identical multidrug resistance profile with co-resistance to trimethoprim/sulfamethoxazole and to aminoglycosides. Plasmid RFLP proved the inter-serovar horizontal spread of a single bla CTX-M- 3-encoding plasmid. Complete sequence of a representative plasmid (S. Havana strain 373.3.1), designated pSEIL-3 was a -86.4 Kb IncM2 plasmid, that encoded nine antibiotic resistance genes. pSEIL-3 was virtually identical to pCTX-M3 from Citrobacter freundii, and showed high identity (>95%) to six other bla CTX-M- 3 or bla NDM- 1 IncM2 broad host range plasmids from various Enterobacterales of human origin. Using a specific six gene-based multiplex PCR, we detected pSEIL-3 in various Enterobacterales species that co-colonized the horses' gut. Together, our findings show the alarming emergence of ESBL-S in hospitalized horses associated with gut shedding and foal morbidity and mortality. We demonstrated the dissemination of CTX-M-3 ESBL among different Salmonella enterica serovars due to transmission of a broad host range plasmid. This report highlights horses as a zoonotic reservoir for ESBL-S, including highly transmissible plasmids that may represent a 'One-Health' hazard. This risk calls for the implementation of infection control measures to monitor and control the spread of ESBL-S in hospitalized horses.
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Affiliation(s)
- Ziv Dor
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Anat Shnaiderman-Torban
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Kira Kondratyeva
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | | | - Assaf Rokney
- Government Central Laboratories, Ministry of Health, Jerusalem, Israel
| | - Amir Steinman
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shiri Navon-Venezia
- Department of Molecular Biology, Ariel University, Ariel, Israel
- The Dr. Miriam and Sheldon G. Adelson School of Medicine, Ariel University, Ariel, Israel
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21
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Lakshmanan R, Kalaimurugan D, Sivasankar P, Arokiyaraj S, Venkatesan S. Identification and characterization of Pseudomonas aeruginosa derived bacteriocin for industrial applications. Int J Biol Macromol 2020; 165:2412-2418. [PMID: 33132130 DOI: 10.1016/j.ijbiomac.2020.10.126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 11/19/2022]
Abstract
Drug resistance has become a major threat due to the frequent use of commercial antibiotics and there is an urgent need to combat this problem. Having this in mind, the present research was aimed at developing a novel P. aeruginosa puBac bacteriocin molecule. The bacteriocin was purified by ammonium sulfate precipitation followed by Sepharose FF and Sephadex G15 column purification and the purified bacteriocin has been reported to have the molar mass of 43 kDa. The findings of the optimization showed that 3500 AU/mL of bacteriocin was obtained at 37 °C, 3410 AU/mL of bacteriocin at 6.5 pH and 3780 AU/mL of bacteriocin at 48 h of incubation time. In addition, 3863 AU/mL of bacteriocin activity was obtained with Tween-80 followed by 3789 AU/mL with a concentration of 2% NaCl and 4200 AU/mL for Fe2+. PuBac bacteriocin has been shown to have a significant effect on test pathogens. For example, E. coli was found to have 3.6 μM of MIC, followed by Staphylococcus sp. with 6.15 μM of MIC and Bacillus sp. with a 7.5 μM of MIC. The remarkable properties of bacteriocin suggest that it could be used in various pharmaceutical and food industries.
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Affiliation(s)
- Ramasamy Lakshmanan
- Department of Environmental Science, School of Life Sciences, Periyar University, Salem 636011, Tamil Nadu, India
| | - Dharman Kalaimurugan
- Department of Environmental Science, School of Life Sciences, Periyar University, Salem 636011, Tamil Nadu, India
| | - Palaniappan Sivasankar
- Department of Environmental Science, School of Life Sciences, Periyar University, Salem 636011, Tamil Nadu, India
| | - Selvaraj Arokiyaraj
- Department of Food Science and Biotechnology, Sejong University, Republic of Korea
| | - Srinivasan Venkatesan
- Department of Environmental Science, School of Life Sciences, Periyar University, Salem 636011, Tamil Nadu, India.
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22
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Park CJ, Li J, Zhang X, Gao F, Benton CS, Andam CP. Diverse lineages of multidrug resistant clinical Salmonella enterica and a cryptic outbreak in New Hampshire, USA revealed from a year-long genomic surveillance. INFECTION GENETICS AND EVOLUTION 2020; 87:104645. [PMID: 33246085 DOI: 10.1016/j.meegid.2020.104645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/11/2020] [Accepted: 11/22/2020] [Indexed: 01/02/2023]
Abstract
Salmonella enterica, the causative agent of gastrointestinal diseases and typhoid fever, is a human and animal pathogen that causes significant mortality and morbidity worldwide. In this study, we examine the genomic diversity and phylogenetic relationships of 63 S. enterica isolates from human-derived clinical specimens submitted to the Department of Health and Human Services (DHHS) in the state of New Hampshire, USA in 2017. We found a remarkably large genomic, phylogenetic and serotype variation among the S. enterica isolates, dominated by serotypes Enteritidis (sequence type [ST] 11), Heidelberg (ST 15) and Typhimurium (ST 19). Analysis of the distribution of single nucleotide polymorphisms in the core genome suggests that the ST 15 cluster is likely a previously undetected or cryptic outbreak event that occurred in the south/southeastern part of New Hampshire in August-September. We found that nearly all of the clinical S. enterica isolates carried horizontally acquired genes that confer resistance to multiple classes of antimicrobials, most notably aminoglycosides, fluoroquinolones and macrolides. Majority of the isolates (76.2%) carry at least four resistance determinants per genome. We also detected the genes mdtK and mdsABC that encode multidrug efflux pumps and the gene sdiA that encodes a regulator for a third multidrug resistance pump. Our results indicate rapid microevolution and geographical dissemination of multidrug resistant lineages over a short time span. These findings are critical to aid the DHHS and similar public health laboratories in the development of effective disease control measures, epidemiological studies and treatment options for serious Salmonella infections.
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Affiliation(s)
- Cooper J Park
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Jinfeng Li
- New Hampshire Department of Health and Human Services, 29 Hazen Drive, Concord, NH, USA
| | - Xinglu Zhang
- New Hampshire Department of Health and Human Services, 29 Hazen Drive, Concord, NH, USA
| | - Fengxiang Gao
- New Hampshire Department of Health and Human Services, 29 Hazen Drive, Concord, NH, USA
| | - Christopher S Benton
- New Hampshire Department of Health and Human Services, 29 Hazen Drive, Concord, NH, USA.
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
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23
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Donoso A, Paredes N, Retamal P. Detection of Antimicrobial Resistant Salmonella enterica Strains in Larval and Adult Forms of Lesser Mealworm ( Alphitobius diaperinus) From Industrial Poultry Farms. Front Vet Sci 2020; 7:577848. [PMID: 33195584 PMCID: PMC7581672 DOI: 10.3389/fvets.2020.577848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/01/2020] [Indexed: 11/13/2022] Open
Abstract
The lesser mealworms (Alphitobius diaperinus) constitute a common cosmopolitan pest in poultry flocks and may colonize the litter in adult and larval forms. Previous studies have documented their potential as carriers of enteric pathogens. In this context, S. enterica constitutes a prioritized zoonotic agent in the poultry industry due to the sanitary risks and economic losses associated with its presence. The aim of this study is to describe the presence of S. enterica strains in larval and adult forms of A. diaperinus collected from poultry litter belonging to industrial farms located in the central zone of Chile. A total of 403 specimens (203 adults and 200 larvae) were sampled from three farms and 25 flocks. For bacteriological isolation, beetles were processed to differentiate external and internal contamination. Then, isolates were serotyped according to the Kauffman-White scheme and antimicrobial resistance phenotypes were determined using the disk diffusion method. Gene sequences from the megaplasmid pESI were identified through a PCR based test. These procedures led to the detection of 15 S. enterica isolates, belonging to serotypes Infantis (14) and Livingstone (1), from both adults (6) and larval (9) specimens, with a similar external (7) and internal (8) distribution. Furthermore, all S. Infantis isolates showed antimicrobial resistance and evidence of megaplasmid pESI carriage, with all possessing multidrug-resistant phenotypes. Our results confirm that A. diaperinus constitutes a potential reservoir of zoonotic Salmonella strains of sanitary and economic concern for the industry and for public health.
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Affiliation(s)
- Alvaro Donoso
- Laboratorio de Enfermedades Infecciosas, Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Natalia Paredes
- Laboratorio de Enfermedades Infecciosas, Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Patricio Retamal
- Laboratorio de Enfermedades Infecciosas, Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
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24
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Wallace MJ, Fishbein SRS, Dantas G. Antimicrobial resistance in enteric bacteria: current state and next-generation solutions. Gut Microbes 2020; 12:1799654. [PMID: 32772817 PMCID: PMC7524338 DOI: 10.1080/19490976.2020.1799654] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Antimicrobial resistance is one of the largest threats to global health and imposes substantial burdens in terms of morbidity, mortality, and economic costs. The gut is a key conduit for the genesis and spread of antimicrobial resistance in enteric bacterial pathogens. Distinct bacterial species that cause enteric disease can exist as invasive enteropathogens that immediately evoke gastrointestinal distress, or pathobionts that can arise from established bacterial commensals to inflict dysbiosis and disease. Furthermore, various environmental reservoirs and stressors facilitate the evolution and transmission of resistance. In this review, we present a comprehensive discussion on circulating resistance profiles and gene mobilization strategies of the most problematic species of enteric bacterial pathogens. Importantly, we present emerging approaches toward surveillance of pathogens and their resistance elements as well as promising treatment strategies that can circumvent common resistance mechanisms.
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Affiliation(s)
- M. J. Wallace
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - S. R. S. Fishbein
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - G. Dantas
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA,CONTACT G. Dantas Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO
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25
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Udaondo Z, Huertas MJ. Fighting the enemy: one health approach against microbial resistance. Microb Biotechnol 2020; 13:888-891. [PMID: 32483942 PMCID: PMC7264875 DOI: 10.1111/1751-7915.13587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 01/03/2023] Open
Abstract
This article highlights publications in Enviromental Microbiology and Microbial Biotechnology papers about antibiotic resistance. It concludes that the One health approach is basic to addressing this problem.
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Affiliation(s)
- Zulema Udaondo
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockAR72205USA
| | - María José Huertas
- Instituto de Bioquímica Vegetal y FotosíntesisUniversidad de Sevilla‐CSICAmérico Vespucio 4941092SevillaSpain
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26
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Dev Kumar G, Mis Solval K, Mishra A, Macarisin D. Antimicrobial Efficacy of Pelargonic Acid Micelles against Salmonella varies by Surfactant, Serotype and Stress Response. Sci Rep 2020; 10:10287. [PMID: 32581319 PMCID: PMC7314784 DOI: 10.1038/s41598-020-67223-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 06/03/2020] [Indexed: 11/08/2022] Open
Abstract
The antimicrobial properties of Pelargonic acid (PA), a component of tomatoes, makes it an attractive candidate as a food additive and sanitizer. The antimicrobial efficacy of PA emulsions generated using surfactants: Tween 80, Triton X100, Sodium Dodecyl Sulfate (SDS) and Quillaja Saponin was evaluated against Salmonella serotypes Newport, Oranienburg and Typhimurium. Micelle/dropletsize, and minimal inhibitory concentrations (MIC) were determined. Surfactant type and concentration significantly influenced the antimicrobial efficacy of PA (p < 0.05). Overall, Salmonella Newport was the most (p < 0.05) susceptible serotype to PA emulsions. PA emulsions generated with 1.00% SDS had the highest (p < 0.05) antimicrobial activity, with MIC of 7.82 mM against S. Newport and 15.62 mM against S. Oranienburg/S. Typhimurium, respectively. Addition of PA to Trypticase Soy Broth resulted in a decreased growth rate and an increased lag phase duration. Cells exposed to PA formed elongated filaments (>5 µm). Additionally, Salmonella serotypes Typhimurium and Newport also formed floccular biofilms. PA emulsions at a concentration of 31.25 mM generated using 1% SDS and 1% Quillaja saponin resulted in >6 log CFU/ml reduction in Salmonella population. Althought all PA emulsions evalauted inhibited Salmonella, morphological changes to this antimicrobial varied substantially among the Salmonella serotypes tested.
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Affiliation(s)
- Govindaraj Dev Kumar
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, USA.
| | - Kevin Mis Solval
- Department of Food Science & Technology, University of Georgia, Griffin, GA, USA
| | - Abhinav Mishra
- Department of Food Science & Technology, University of Georgia, Athens, GA, USA
| | - Dumitru Macarisin
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA.
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27
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Palma E, Tilocca B, Roncada P. Antimicrobial Resistance in Veterinary Medicine: An Overview. Int J Mol Sci 2020; 21:E1914. [PMID: 32168903 PMCID: PMC7139321 DOI: 10.3390/ijms21061914] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance (AMR) represents one of the most important human- and animal health-threatening issues worldwide. Bacterial capability to face antimicrobial compounds is an ancient feature, enabling bacterial survival over time and the dynamic surrounding. Moreover, bacteria make use of their evolutionary machinery to adapt to the selective pressure exerted by antibiotic treatments, resulting in reduced efficacy of the therapeutic intervention against human and animal infections. The mechanisms responsible for both innate and acquired AMR are thoroughly investigated. Commonly, AMR traits are included in mobilizable genetic elements enabling the homogeneous diffusion of the AMR traits pool between the ecosystems of diverse sectors, such as human medicine, veterinary medicine, and the environment. Thus, a coordinated multisectoral approach, such as One-Health, provides a detailed comprehensive picture of the AMR onset and diffusion. Following a general revision of the molecular mechanisms responsible for both innate and acquired AMR, the present manuscript focuses on reviewing the contribution of veterinary medicine to the overall issue of AMR. The main sources of AMR amenable to veterinary medicine are described, driving the attention towards the indissoluble cross-talk existing between the diverse ecosystems and sectors and their cumulative cooperation to this warning phenomenon.
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Affiliation(s)
| | | | - Paola Roncada
- Department of Health Science, University “Magna Graecia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (E.P.); (B.T.)
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