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Li X, Mowlaboccus S, Jackson B, Cai C, Coombs GW. Antimicrobial Resistance Among Clinically Significant Bacteria in Wildlife: An Overlooked One Health Concern. Int J Antimicrob Agents 2024; 64:107251. [PMID: 38906487 DOI: 10.1016/j.ijantimicag.2024.107251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 06/23/2024]
Abstract
Antimicrobial resistance (AMR) has emerged as a critical global health challenge. However, the significance of AMR is not limited to humans and domestic animals but extends to wildlife and the environment. Based on the analysis of > 200 peer-reviewed papers, this review provides comprehensive and current insights into the detection of clinically significant antimicrobial resistant bacteria and resistance genes in wild mammals, birds and reptiles worldwide. The review also examines the overlooked roles of wildlife in AMR emergence and transmission. In wildlife, AMR is potentially driven by anthropogenic activity, agricultural and environmental factors, and natural evolution. This review highlights the significance of AMR surveillance in wildlife, identifies species and geographical foci and gaps, and demonstrates the value of multifaceted One Health strategies if further escalation of AMR globally is to be curtailed.
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Affiliation(s)
- Xing Li
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia; Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Perth, Australia
| | - Bethany Jackson
- School of Veterinary Medicine, Murdoch University, Perth, Australia
| | - Chang Cai
- School of Information Technology, College of Science, Technology, Engineering and Mathematics, Murdoch University, Perth, Australia
| | - Geoffrey Wallace Coombs
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia; Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Perth, Australia.
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Brek T, Gohal GA, Yasir M, Azhar EI, Al-Zahrani IA. Meningitis and Bacteremia by Unusual Serotype of Salmonella enterica Strain: A Whole Genome Analysis. Interdiscip Perspect Infect Dis 2024; 2024:3554734. [PMID: 38558876 PMCID: PMC10980553 DOI: 10.1155/2024/3554734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/27/2023] [Accepted: 03/17/2024] [Indexed: 04/04/2024] Open
Abstract
Background Although meningitis caused by Salmonella species is relatively rare and accounts for <1% of the confirmed cases in neonates, it is associated with case complications and fatality rates up to 50-70% when compared to other forms of Gram-negative bacilli meningitis. Objectives We conducted an investigation into the first reported case of neonatal meningitis caused by nontyphoidal S. enterica in Jazan, a region in the southwestern part of Saudi Arabia. Methods CSF and blood culture were collected from a female neonate patient to confirm the presence of bacterial meningitis. WGS was conducted to find out the comprehensive genomic characterization of S. enterica isolate. Results A 3-week-old infant was admitted to a local hospital with fever, poor feeding, and hypoactivity. She was diagnosed with Salmonella meningitis and bacteremia caused by S. enterica, which was sensitive to all antimicrobials tested. WGS revealed the specific strain to be S. enterica serotype Johannesburg JZ01, belonging to ST515 and cgMLST 304742. Conclusions We presented a genomic report of rare case of NTS meningitis in an infant who is living in a rural town in Jazan region, Saudi Arabia. Further research is required to understand the impact of host genetic factors on invasive nontyphoidal Salmonella infection.
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Affiliation(s)
- Thamer Brek
- Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Public Health Laboratory, The Regional Laboratory and the Central Blood Bank, Jazan Health Directorate, Jazan, Saudi Arabia
| | - Gassem A. Gohal
- Department of Pediatrics, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia
| | - Muhammad Yasir
- Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Special Infectious Agents Unit-Biosafety Level-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I. Azhar
- Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Special Infectious Agents Unit-Biosafety Level-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ibrahim A. Al-Zahrani
- Medical Laboratory Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Special Infectious Agents Unit-Biosafety Level-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
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Cummings KJ, Siler JD, Goodman LB, Childs-Sanford SE. Ciprofloxacin-resistant ST198 Salmonella Kentucky in a hospitalized American black bear (Ursus americanus), with evidence of subsequent nosocomial transmission. Zoonoses Public Health 2023; 70:657-664. [PMID: 37464973 DOI: 10.1111/zph.13075] [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: 12/20/2022] [Revised: 06/01/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023]
Abstract
Global emergence of ciprofloxacin-resistant ST198 Salmonella Kentucky poses an important public health threat. While conducting Salmonella surveillance among wildlife patients admitted to our veterinary medical teaching hospital in central New York, we isolated multidrug-resistant (MDR) ST198 Salmonella Kentucky from an American black bear (Ursus americanus) in September 2020. The isolate was phenotypically resistant to numerous antimicrobial agents, including ceftriaxone and ciprofloxacin, and several antimicrobial resistance genes and mutational resistance determinants were detected. Between April and July 2021, the same strain of MDR ST198 Salmonella Kentucky was also isolated from seven other wildlife patients and multiple hospital environmental locations, suggesting nosocomial transmission. Ciprofloxacin resistance is conferred by triple point mutations in the quinolone resistance-determining regions (QRDRs), a genotypic profile indicative of Clade ST198.2. To our knowledge, this is the first report of this ciprofloxacin-resistant clade being identified in animals or animal products in the United States. Timely resolution of the outbreak was achieved following efforts to further enhance environmental disinfection protocols and biosecurity measures at the hospital, with no known cases or positive environmental samples after July 2021.
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Bellil Z, Meyer S, Tilloy V, Mairi A, Barraud O, De Champs C, Touati A. Comprehensive Genomic Characterization of Antibiotic Resistance, Virulence, and Clonality in Salmonella Isolates from Wild Animals in Algeria. ECOHEALTH 2023; 20:343-348. [PMID: 38177562 DOI: 10.1007/s10393-023-01670-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
This study investigated Salmonella spp. in wild animals in Algeria, focusing on their prevalence, serotypes, antibiotic resistance, and virulence profiles. From fecal samples collected between May 2021 and June 2022, 1.9% showed Salmonella shedding. The identified serotypes included S. Bredeney, S. Enteritidis, S. Altona, and S. Virchow. Except for S. Altona, all isolates were resistant to quinolones, with S. Bredeney strains, exhibiting multidrug resistance. Whole-genome sequencing revealed various resistance genes and mutations in gyrA or parC genes. Additionally, plasmids IncX1 and ColpVC were detected in several isolates. A comprehensive analysis identified 201 virulence genes. These findings contribute to understanding Salmonella in wild animal populations and their potential impact on public health.
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Affiliation(s)
- Zahra Bellil
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Béjaïa, Algeria
| | - Sylvain Meyer
- INSERM, CHU Limoges, RESINFIT, Université de Limoges, U1092, Limoges, France
| | - Valentin Tilloy
- CNR Herpesvirus, UF 9481 Bioinformatique, CHU Limoges, Limoges, France
| | - Assia Mairi
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Béjaïa, Algeria
| | - Olivier Barraud
- INSERM, CHU Limoges, RESINFIT, Université de Limoges, U1092, Limoges, France
| | - Christophe De Champs
- INSERM UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, Reims, France
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, Hôpital Robert Debré, CHU Reims, Reims, France
| | - Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Béjaïa, Algeria.
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Fu Y, M’ikanatha NM, Dudley EG. Whole-Genome Subtyping Reveals Population Structure and Host Adaptation of Salmonella Typhimurium from Wild Birds. J Clin Microbiol 2023; 61:e0184722. [PMID: 37249426 PMCID: PMC10281135 DOI: 10.1128/jcm.01847-22] [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: 12/14/2022] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Within-host evolution of bacterial pathogens can lead to host-associated variants of the same species or serovar. Identification and characterization of closely related variants from diverse host species are crucial to public health and host-pathogen adaptation research. However, the work remained largely underexplored at a strain level until the advent of whole-genome sequencing (WGS). Here, we performed WGS-based subtyping and analyses of Salmonella enterica serovar Typhimurium (n = 787) from different wild birds across 18 countries over a 75-year period. We revealed seven avian host-associated S. Typhimurium variants/lineages. These lineages emerged globally over short timescales and presented genetic features distinct from S. Typhimurium lineages circulating among humans and domestic animals. We further showed that, in terms of virulence, host adaptation of these variants was driven by genome degradation. Our results provide a snapshot of the population structure and genetic diversity of S. Typhimurium within avian hosts. We also demonstrate the value of WGS-based subtyping and analyses in unravelling closely related variants at the strain level.
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Affiliation(s)
- Yezhi Fu
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Edward G. Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- E. coli Reference Center, The Pennsylvania State University, University Park, Pennsylvania, USA
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Tang B, Siddique A, Jia C, Ed-Dra A, Wu J, Lin H, Yue M. Genome-based risk assessment for foodborne Salmonella enterica from food animals in China: A One Health perspective. Int J Food Microbiol 2023; 390:110120. [PMID: 36758302 DOI: 10.1016/j.ijfoodmicro.2023.110120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 02/06/2023]
Abstract
Salmonella is one of the most common causes of foodborne bacterial disease. Animal-borne foods are considered the primary sources of Salmonella transmission to humans. However, genomic assessment of antimicrobial resistance (AMR) and virulence of Salmonella based on One Health approach remains obscure in China. For this reason, we analyzed the whole genome sequencing data of 134 Salmonella isolates recovered from different animal and meat samples in China. The 134 Salmonella were isolated from 2819 samples (4.75 %) representing various sources (pig, chicken, duck, goose, and meat) from five Chinese provinces (Zhejiang, Guangdong, Jiangxi, Hunan, and Qinghai). AMR was evaluated by the broth dilution method using 13 different antimicrobial agents, and results showed that 85.82 % (115/134) of isolates were resistant to three or more antimicrobial classes and were considered multidrug-resistant (MDR). Twelve sequence types (STs) were detected, with a dominance of ST469 (29.85 %, 40/134). The prediction of virulence genes showed the detection of cdtB gene encoding typhoid toxins in one isolate of S. Muenster recovered from chicken, while virulence genes associated with type III secretion systems were detected in all isolates. Furthermore, plasmid-type prediction showed the abundance of IncFII(S) (13/134; 9.7 %) and IncFIB(S) (12/134; 8.95 %) in the studied isolates. Together, this study demonstrated the ability to use whole-genome sequencing (WGS) as a cost-effective method to provide comprehensive knowledge about foodborne Salmonella isolates in One Health surveillance approach.
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Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Abubakar Siddique
- Hainan Institute of Zhejiang University, Sanya 572025, China; Atta Ur Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad 44000, Pakistan
| | - Chenhao Jia
- Hainan Institute of Zhejiang University, Sanya 572025, China; Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Jing Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Min Yue
- Hainan Institute of Zhejiang University, Sanya 572025, China; Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China.
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Souza SSR, Turcotte MR, Li J, Zhang X, Wolfe KL, Gao F, Benton CS, Andam CP. Population analysis of heavy metal and biocide resistance genes in Salmonella enterica from human clinical cases in New Hampshire, United States. Front Microbiol 2022; 13:983083. [PMID: 36338064 PMCID: PMC9626534 DOI: 10.3389/fmicb.2022.983083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
Microbes frequently encounter heavy metals and other toxic compounds generated from natural biogeochemical processes and anthropogenic activities. Here, we analyzed the prevalence and association of genes conferring resistance to heavy metals, biocides, and antimicrobial compounds in 394 genome sequences of clinical human-derived S. enterica from New Hampshire, USA. The most prevalent was the gold operon (gesABC-golTSB), which was present in 99.2% of the genomes. In contrast, the other five heavy metal operons (arsenic, copper, mercury, silver, tellurite) were present in 0.76% (3/394)–5.58% (22/394) of the total population. The heavy metal operons and three biocide resistance genes were differentially distributed across 15 sequence types (STs) and 16 serotypes. The number of heavy metal operons and biocide resistance genes per genome was significantly associated with high number of antimicrobial resistance (AMR) genes per genome. Notable is the mercury operon which exhibited significant association with genes conferring resistance to aminoglycosides, cephalosporins, diaminopyrimidine, sulfonamide, and fosfomycin. The mercury operon was co-located with the AMR genes aac(3)-IV, ant(3”)-IIa, aph(3’)-Ia, and aph(4)-Ia, CTX-M-65, dfrA14, sul1, and fosA3 genes within the same plasmid types. Lastly, we found evidence for negative selection of individual genes of each heavy metal operon and the biocide resistance genes (dN/dS < 1). Our study highlights the need for continued surveillance of S. enterica serotypes that carry those genes that confer resistance to heavy metals and biocides that are often associated with mobile AMR genes. The selective pressures imposed by heavy metals and biocides on S. enterica may contribute to the co-selection and spread of AMR in human infections.
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Affiliation(s)
- Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
- *Correspondence: Stephanie S. R. Souza, ; orcid.org/0000-0002-4207-8231
| | - Madison R. Turcotte
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
| | - Jinfeng Li
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Xinglu Zhang
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Kristin L. Wolfe
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Fengxiang Gao
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | | | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
- Cheryl P. Andam, ; orcid.org/0000-0003-4428-0924
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Comparative Genomic Analysis of Salmonella enterica Serovar Typhimurium Isolates from Passerines Reveals Two Lineages Circulating in Europe, New Zealand, and the United States. Appl Environ Microbiol 2022; 88:e0020522. [PMID: 35435718 DOI: 10.1128/aem.00205-22] [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] [Indexed: 02/03/2023] Open
Abstract
Salmonella enterica serovar Typhimurium strains from passerines have caused wild bird deaths and human salmonellosis outbreaks in Europe, Oceania, and North America. Here, we performed comparative genomic analysis to explore the emergence, genetic relationship, and evolution of geographically dispersed passerine isolates. We found that passerine isolates from Europe and the United States clustered to form two lineages (EU and US passerine lineages), which were distinct from major S. Typhimurium lineages circulating in other diverse hosts (e.g., humans, cattle, pigs, chickens, and other avian hosts, such as pigeons and ducks). Further, passerine isolates from New Zealand clustered to form a sublineage (NZ passerine lineage) of the US passerine lineage. We inferred that the passerine isolates mutated at a rate of 3.2 × 10-7 substitutions/site/year, and the US, EU, and NZ passerine lineages emerged in approximately 1952, 1970, and 1996, respectively. Isolates from the three lineages presented genetic similarity, such as lack of antimicrobial resistance genes and accumulation of the same virulence pseudogenes. In addition, genetic diversity due to microevolution existed in the three passerine lineages. Specifically, pseudogenization in the type 1 fimbrial gene fimC (deletion of G at position 87) was detected only in the US and NZ passerine isolates, while single-base deletions in type 3 secretion system effector genes (i.e., gogB, sseJ, and sseK2) cooccurred solely in the EU passerine isolates. These findings provide insights into the evolution, host adaptation, and epidemiology of S. Typhimurium in passerines. IMPORTANCE Passerine-associated S. Typhimurium strains have been linked to human salmonellosis outbreaks in recent years. Here, we investigated the phylogenetic relationship of globally distributed passerine isolates and profiled their genomic similarity and diversity. Our study reveals two passerine-associated S. Typhimurium lineages circulating in Europe, Oceania, and North America. Isolates from the two lineages presented phylogenetic and genetic signatures that were distinct from those of isolates from other hosts. The findings shed light on the host adaptation of S. Typhimurium in passerines and are important for source attribution of S. Typhimurium strains to avian hosts. Further, we found that S. Typhimurium definitive phage type 160 (DT160) from passerines, which caused decades-long human salmonellosis outbreaks in New Zealand and Australia, formed a sublineage of the US passerine lineage, suggesting that DT160 might have originated from passerines outside Oceania. Our study demonstrates the importance of whole-genome sequencing and genomic analysis of historical microbial collections to modern epidemiologic surveillance.
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Fu Y, Smith JC, Shariat NW, M'ikanatha NM, Dudley EG. Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA. Microb Genom 2022; 8. [PMID: 35195512 PMCID: PMC8942035 DOI: 10.1099/mgen.0.000775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The evolution of Salmonella enterica serovar Typhimurium (S. Typhimurium) within passerines has resulted in pathoadaptation of this serovar to the avian host in Europe. Recently, we identified an S. Typhimurium lineage from passerines in North America. The emergence of passerine-adapted S. Typhimurium in Europe and North America raises questions regarding its evolutionary origin. Here, we demonstrated that the UK and US passerine-adapted S. Typhimurium shared a common ancestor from ca. 1838, and larids played a key role in the clonal expansion by disseminating the common ancestor between North America and Europe. Further, we identified virulence gene signatures common in the passerine- and larid-adapted S. Typhimurium, including conserved pseudogenes in fimbrial gene lpfD and Type 3 Secretion System (T3SS) effector gene steC. However, the UK and US passerine-adapted S. Typhimurium also possessed unique virulence gene signatures (i.e. pseudogenes in fimbrial gene fimC and T3SS effector genes sspH2, gogB, sseJ and sseK2), and the majority of them (38/47) lost a virulence plasmid pSLT that was present in the larid-adapted S. Typhimurium. These results provide evidence that passerine-adapted S. Typhimurium share a common ancestor with those from larids, and the divergence of passerine- and larid-adapted S. Typhimurium might be due to pseudogenization or loss of specific virulence genes.
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Affiliation(s)
- Yezhi Fu
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jared C Smith
- Department of Population Health, Poultry Diagnostic and Research Center, University of Georgia, Athens, GA 30602, USA
| | - Nikki W Shariat
- Department of Population Health, Poultry Diagnostic and Research Center, University of Georgia, Athens, GA 30602, USA
| | | | - Edward G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA.,E. coli Reference Center, The Pennsylvania State University, University Park, PA 16802, USA
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