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Antibiotic Resistance and Infectious Diseases: A One Health Perspective

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A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 34519

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Dr. Alain Antonio Ocampo-Sosa

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Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39008 Santander, Spain
Interests: antimicrobial resistance; infectious disease; gram-negative pathogens; pseudomonas aeruginosa; klebsiella pneumoniae; biofilm; host-pathogens interactions; bacterial genomics

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) is a very complex, multifaceted matter that poses a threat for human, animal health, economy and security worldwide. The indiscriminate use of antibiotics in human clinical practice and also in veterinary and animal production is the main cause of the problem. AMR should be managed from a One Health perception, integrating comprehensive information regarding the correct use of antibiotics in humans, animals and food chain, but also dealing with the environment, as wildlife ecosystems are potential reservoirs for multidrug-resistant (MDR) microorganisms and antimicrobial resistant genes (ARG). Examples that highlight the risk of rapid dissemination of ARG are the presence of plasmid-encoded carbapenemase and colistin resistance mcr genes, which are now showing their worldwide spread variants. It is essential to include the information collected from animal and food chain pathogens into AMR surveillance programs as a part of the One Health framework, since human and animal health is interconnected. In that sense, whole-genome sequencing (WGS) has become an essential tool to identify and understand the origin and spread of AMR and for establishing successful One Health surveillance strategies.

This Special Issue will focus on antimicrobial resistance in clinically relevant human pathogens but also animal and food borne transmitted infectious diseases. We encourage the submission of interdisciplinary work and multi-centre collaborative research. Original research papers using different study designs as well as literature review and meta-analysis are welcome.

Dr. Alain Antonio Ocampo-Sosa
Guest Editor

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

antimicrobial resistance
infectious diseases
One Health
multidrug-resistance (MDR)
AMR surveillance
whole-genome sequence (WGS)

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Published Papers (11 papers)

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Research

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18 pages, 1518 KiB

Open AccessArticle

Prevalence and Antimicrobial Resistance of Virulent Listeria monocytogenes and Cronobacter sakazakii in Dairy Cattle, the Environment, and Dried Milk with the In Vitro Application of Natural Alternative Control

by Basma Badawy, Mayada Gwida, Asmaa Sadat, Marwa EL-Toukhy, Mohamed Sayed-Ahmed, Nawazish Alam, Sarfaraz Ahmad, MD Sajid Ali and Mahmoud Elafify

Antibiotics 2022, 11(8), 1087; https://doi.org/10.3390/antibiotics11081087 - 10 Aug 2022

Cited by 14 | Viewed by 2549

Abstract

This study aims to detect the prevalence and antimicrobial resistance of Listeria monocytogenes and Cronobacter sakazakii in three dairy households and dried milk from different suppliers, and evaluate the antimicrobial effect of rose water, rose, and orange essential oils. In total, 360 samples were collected from cattle, the environment, and dried milk (n = 30). Antimicrobial activity was evaluated with twofold microtube dilution and the time-kill method. L. monocytogenes was identified in all households (13.3%) with a prevalence in the range of 5.8–17.5%, while C. sakazakii was identified in one household (5.3%). The former and latter pathogens were highly isolated from the feces at 20% and 2.5% and bedding at 12.5% and 1.6%, respectively. L. monocytogenes was isolated only from milk at 7.5%, but C. sakazakii was not detected in either milk or dried milk. L. monocytogenes strains were screened for virulence genes (iap, hylA, and actA). All strains were positive for the iap gene, while for hlyA and actA, the percentages were (35.4% 16.6%, respectively). L. monocytogenes strains showed high resistance against sulfamethoxazole–trimethoprim (100%), followed by gentamicin, penicillin, and imipenem (95.8%, 95.8%, and 91.6%, respectively). All C. sakazakii strains were susceptible to all tested antibiotics. The bactericidal activity of orange oil was the strongest, appeared after 1 h for both pathogens, followed by rose oil and then rose water. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

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11 pages, 311 KiB

Open AccessArticle

Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru

by Maria Luisa Medina-Pizzali, Apoorva Venkatesh, Maribel Riveros, Diego Cuicapuza, Gabriela Salmon-Mulanovich, Daniel Mäusezahl and Stella M. Hartinger

Antibiotics 2022, 11(5), 692; https://doi.org/10.3390/antibiotics11050692 - 20 May 2022

Cited by 9 | Viewed by 3430

Abstract

E. coli that produce extended-spectrum β-lactamases (ESBLs) are major multidrug-resistant bacteria. In Peru, only a few reports have characterised the whole genome of ESBL enterobacteria. We aimed to confirm the identity and antimicrobial resistance (AMR) profile of two ESBL isolates from dog faeces and drinking water of rural Andean households and determine serotype, phylogroup, sequence type (ST)/clonal complex (CC), pathogenicity, virulence genes, ESBL genes, and their plasmids. To confirm the identity and AMR profiles, we used the VITEK^®2 system. Whole-genome sequencing (WGS) and bioinformatics analysis were performed subsequently. Both isolates were identified as E. coli, with serotypes -:H46 and O9:H10, phylogroups E and A, and ST/CC 5259/- and 227/10, respectively. The isolates were ESBL-producing, carbapenem-resistant, and not harbouring carbapenemase-encoding genes. Isolate 1143 ST5259 harboured the astA gene, encoding the EAST₁ heat-stable toxin. Both genomes carried ESBL genes (bla_EC-15, bla_CTX-M-8, and bla_CTX-M-55). Nine plasmids were detected, namely IncR, IncFIC(FII), IncI, IncFIB(AP001918), Col(pHAD28), IncFII, IncFII(pHN7A8), IncI1, and IncFIB(AP001918). Finding these potentially pathogenic bacteria is worrisome given their sources and highlights the importance of One-Health research efforts in remote Andean communities. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

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13 pages, 516 KiB

Open AccessArticle

Transmission of Methicillin-Resistant Staphylococcus spp. from Infected Dogs to the Home Environment and Owners

by Mari Røken, Stanislav Iakhno, Anita Haug Haaland, Yngvild Wasteson and Ane Mohn Bjelland

Antibiotics 2022, 11(5), 637; https://doi.org/10.3390/antibiotics11050637 - 10 May 2022

Cited by 10 | Viewed by 2556

Abstract

Dogs with methicillin-resistant Staphylococcus spp. (MRS) infections often undergo treatment in their homes, interacting with their owners and surroundings. This close contact between dogs and owners may facilitate the interspecies transmission of MRS. Therefore, this study aimed to investigate the transmission of MRS from infected dogs to their owners and home environments. Seven households with dogs that had been diagnosed with methicillin-resistant S. pseudintermedius (MRSP) and one household with a dog with methicillin-resistant S. epidermidis (MRSE) participated in the study. Dogs, owners, and the home environments were screened for the presence of clinical MRS. A selection of 36 staphylococcal isolates were whole-genome sequenced and screened for resistance genes and virulence genes. Clinical MRS were primarily identified from the dogs and their immediate surroundings, but these were also detected in locations that were out of reach for the dogs, indicating indirect transmission. Two of eight owners carried clinical MRS in their nostrils, while one owner carried methicillin-susceptible S. pseudintermedius (MSSP). All clinical MRS were multi-resistant, and several possessed resistance genes that were not expressed phenotypically. Clinical MRSP persisted in the home environment for a prolonged period, despite infection recovery and one dog being euthanized. Regardless of the stable presence of MRSP in the surroundings, the owners in these homes remained negative, but tested positive for MSSP on three occasions. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

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10 pages, 243 KiB

Open AccessArticle

One Health Surveillance of Antimicrobial Resistance Phenotypes in Selected Communities in Thailand

by Duangdao Sudatip, Surapee Tiengrim, Kittipong Chasiri, Anamika Kritiyakan, Wantanee Phanprasit, Serge Morand and Visanu Thamlikitkul

Antibiotics 2022, 11(5), 556; https://doi.org/10.3390/antibiotics11050556 - 21 Apr 2022

Cited by 5 | Viewed by 2468

Abstract

Integrated surveillance of antimicrobial resistance (AMR) using the One Health approach that includes humans, animals, food, and the environment has been recommended by responsible international organizations. The objective of this study was to determine the prevalence of AMR phenotypes in Escherichia coli and Klebsiella species isolated from humans, pigs, chickens, and wild rodents in five communities in northern Thailand. Rectal swabs from 269 pigs and 318 chickens; intestinal contents of 196 wild rodents; and stool samples from 69 pig farmers, 155 chicken farmers, and 61 non-farmers were cultured for E. coli and Klebsiella species, which were then tested for resistance to ceftriaxone, colistin, and meropenem. The prevalence of ceftriaxone-resistant E. coli and Klebsiella species in pigs, chickens, rodents, pig farmers, chicken farmers, and non-farmers was 64.3%, 12.9%, 4.1%, 55.1%, 38.7%, and 36.1%, respectively. Colistin resistance in pigs, chickens, rodents, pig farmers, chicken farmers, and non-farmers was 41.3%, 9.8%, 4.6%, 34.8%, 31.6%, and 24.6%, respectively. Meropenem resistance was not detected. The observed high prevalence of AMR, especially colistin resistance, in study food animals/humans is worrisome. Further studies to identify factors that contribute to AMR, strengthened reinforcement of existing regulations on antimicrobial use, and more appropriate interventions to minimize AMR in communities are urgently needed. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

15 pages, 1223 KiB

Open AccessArticle

Prevalence and Characteristics of Streptococcus agalactiae from Freshwater Fish and Pork in Hong Kong Wet Markets

by Dulmini Nanayakkara Sapugahawatte, Carmen Li, Priyanga Dharmaratne, Chendi Zhu, Yun Kit Yeoh, Jun Yang, Norman Wai Sing Lo, Kam Tak Wong and Margaret Ip

Antibiotics 2022, 11(3), 397; https://doi.org/10.3390/antibiotics11030397 - 16 Mar 2022

Cited by 14 | Viewed by 3596

Abstract

We report the antimicrobial resistance of 191 fish and 61 pork Group B Streptococcus (GBS) procured from Hong Kong wet markets. Two-hundred-and-fifty-two GBS strains were isolated from 992 freshwater fish and 361 pig offal during 2016–2019. The strains were isolated from homogenised samples and plated on selective media, followed by identification through MALDI-TOF-MS. Molecular characterisation, an antibiotic susceptibility test, and biofilm formation were performed on the strains. The isolation rates of the fish GBS and pig GBS were 19.3% (191 strains from 992 freshwater fish) and 16.9% (61 strains from 361 pig organs), respectively. The fish GBS was predominantly serotype Ia, ST7, while pig GBS was serotype III, ST651 (45 strains). An antibiotic susceptibility test revealed that the fish GBS were mostly antibiotic-sensitive, while the pig GBS were multidrug-resistant. A biofilm formation experiment showed that over 71% of fish GBS and all pig GBS had moderate biofilm formation ability. In general, the prevalence rate of GBS in animals and the multidrug resistance phenotype presented in the strains raise concerns about its zoonotic potential and effects on public health. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

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10 pages, 998 KiB

Open AccessArticle

One Health Genomic Study of Human and Animal Klebsiella pneumoniae Isolated at Diagnostic Laboratories on a Small Caribbean Island

by Patrick Butaye, Marc Stegger, Arshnee Moodley, Peter Damborg, Andrea Williams, Iona Halliday-Simmonds and Luca Guardabassi

Antibiotics 2022, 11(1), 42; https://doi.org/10.3390/antibiotics11010042 - 30 Dec 2021

Cited by 10 | Viewed by 2535

Abstract

Klebsiella pneumoniae causes a variety of infections in both humans and animals. In this study, we characterised the genomes of human and animal isolates from two diagnostic laboratories on St. Kitts, a small Caribbean island inhabited by a large population of vervet monkeys. In view of the increased chances of direct or indirect contact with humans and other animal species, we used the One Health approach to assess transmission of K. pneumoniae across host species by sequencing 82 presumptive K. pneumoniae clinical isolates from humans (n = 51), vervets (n = 21), horses (n = 5), dogs (n = 4) and a cat (n = 1). Whole genome sequencing (WGS) was carried out using Illumina technology. De novo assembly was performed in CLC Genomics Workbench v.11.0. Single nucleotide polymorphisms were detected using NASP followed by phylogenetic analysis using IQ-TREE. Virulence and antimicrobial resistance gene contents were analysed using the Kleborate and CGE pipelines. WGS-based analysis showed that 72 isolates were K. pneumoniae sensu stricto and five K. quasipneumoniae and five K. variicola. K. pneumoniae isolates belonged to 35 sequence types (ST), three of which were occasionally shared between humans and animals: ST23, ST37 and ST307. The ST23 strains from vervets formed a separate cluster amongst publicly available sequenced ST23 strains, indicating the presence of a specific vervet sublineage. Animal strains harbored fewer resistance genes and displayed distinct virulence traits that appeared to be host-specific in vervet isolates. Our results show that K. pneumoniae infections on this Caribbean island are usually caused by host-specific lineages. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

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7 pages, 251 KiB

Open AccessArticle

Prevalence and Molecular Epidemiology of Extended-Spectrum-β-Lactamase (ESBL)-Producing Escherichia coli from Multiple Sectors of Poultry Industry in Korea

by Hyunsoo Kim, Young Ah Kim, Young Hee Seo, Hyukmin Lee and Kyungwon Lee

Antibiotics 2021, 10(9), 1050; https://doi.org/10.3390/antibiotics10091050 - 28 Aug 2021

Cited by 12 | Viewed by 2933

Abstract

The aim of this study was to investigate the molecular epidemiology of extended-spectrum-β-lactamase producing Escherichia coli (ESBL-EC) from poultry, the poultry farm environment, and workers in Korea. A total of 1376 non-duplicate samples were collected from 21 poultry farms, 20 retail stores, 6 slaughterhouses, and 111 workers in a nationwide study in Korea from January 2019 to August 2019. The overall positive rate of ESBL-EC was 6.8%, with variable positive rates according to sources (0.9% of worker, 5.2% of poultry, 10.0% of chicken meat, and 14.3% of environment). Common ESBL types were CTX-M-55 and CTX-M-14 in a total of 93 ESBL-EC isolates. Whole genome sequencing revealed that 84 ESBL-EC isolates had an outstanding accumulation of numerous antimicrobial resistance (AMR) genes associated with resistance to various classes of antimicrobials for human use and well-known antimicrobial gene (ARG)-carrying plasmids. Core gene multi locus sequence typing, using 2390 core genes, indicated no dominant clone or common type in each province. In conclusion, the isolation rates of ESBL-EC were not negligible in the poultry industry-related samples, sharing common ESBL types of human ESBL-EC isolates in Korea. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

10 pages, 1587 KiB

Open AccessArticle

Colistin Selection of the Mcr-1 Gene in Broiler Chicken Intestinal Microbiota

by Pedro Miguela-Villoldo, Miguel A. Moreno, Agustín Rebollada-Merino, Antonio Rodríguez-Bertos, Marta Hernández, David Rodríguez-Lázaro, Alejandro Gallardo, Alberto Quesada, Joaquín Goyache, Lucas Domínguez and María Ugarte-Ruiz

Antibiotics 2021, 10(6), 677; https://doi.org/10.3390/antibiotics10060677 - 5 Jun 2021

Cited by 2 | Viewed by 2954

Abstract

Colistin has a long story of safe use in animals for the treatment and prevention of certain bacterial diseases. Nevertheless, the first description of the mcr-1 gene showed that colistin resistance can spread by horizontal gene transfer and changed the landscape. This study aimed to assess the effect of colistin administration on the dispersion of resistance in the microbiota of day-old broiler chicks and how the presence of mcr-1 genes influences the spread of colistin resistance determinants. In this study, 100 one-day-old chicks were divided into four groups of 25 animals (G1, G2, G3, and G4). Animals from G3/G4 were challenged with mcr-1-carrying Salmonella (day 7), while colistin (600 mg/L) was administered daily to G2/G4 animals through drinking water (from day 8 to day 15). Two quantitative PCR assays were performed to compare the amount of Salmonella and mcr-1 that were present in the caecal samples. We observed that levels of mcr-1 were higher in G3/G4 animals, especially G4, due to the spread of mcr-1-carrying Salmonella. On day 21, Salmonella levels decreased in G4, reaching similar values as those for G3, but mcr-1 levels remained significantly higher, suggesting that colistin may accelerate the spreading process when mcr-1-carrying bacteria reach the gut. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

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Review

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11 pages, 1444 KiB

Open AccessReview

The Emergence and Dissemination of Multidrug Resistant Pseudomonas aeruginosa in Lebanon: Current Status and Challenges during the Economic Crisis

by Ahmad Ayman Dabbousi, Fouad Dabboussi, Monzer Hamze, Marwan Osman and Issmat I. Kassem

Antibiotics 2022, 11(5), 687; https://doi.org/10.3390/antibiotics11050687 - 19 May 2022

Cited by 13 | Viewed by 3641

Abstract

Pseudomonas aeruginosa is a common cause of healthcare-associated infections and chronic airway diseases in non-clinical settings. P. aeruginosa is intrinsically resistant to a variety of antimicrobials and has the ability to acquire resistance to others, causing increasingly recalcitrant infections and elevating public health concerns. We reviewed the literature on multidrug-resistant (MDR) P. aeruginosa isolated from humans (nosocomial and community-associated), animals, and the environment in Lebanon, a country that has been suffering from a surge in antimicrobial resistance (AMR). We identified 24 studies that described the epidemiology and antimicrobial susceptibility profiles of P. aeruginosa. Our analysis showed that the bacterium was predominant in lesions of patients on mechanical ventilation and in burn patients and those with diabetic foot infections and hematological malignancies. We also found that carbapenem resistance in P. aeruginosa isolates in Lebanon involved both enzymatic and non-enzymatic mechanisms but depended predominantly on VIM-2 production (40.7%). Additionally, MDR P. aeruginosa was detected in animals, where a recent study reported the emergence of carbapenemase-producing P. aeruginosa in livestock in Lebanon. Notably, no studies evaluated the contribution of MDR P. aeruginosa in the environment to human infections. Taken together, our findings highlight the need for AMR surveillance programs and a national action plan to combat resistance in Lebanon. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

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Other

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6 pages, 381 KiB

Open AccessBrief Report

Concentrations of Ciprofloxacin in the World’s Rivers Are Associated with the Prevalence of Fluoroquinolone Resistance in Escherichia coli: A Global Ecological Analysis

by Chris Kenyon

Antibiotics 2022, 11(3), 417; https://doi.org/10.3390/antibiotics11030417 - 20 Mar 2022

Cited by 9 | Viewed by 2872

Abstract

Background: Extremely low concentrations of ciprofloxacin may select for antimicrobial resistance. A recent global survey found that ciprofloxacin concentrations exceeded safe levels at 64 sites. In this study, I assessed if national median ciprofloxacin concentrations in rivers were associated with fluoroquinolone resistance in Escherichia coli. Methods: Spearman’s regression was used to assess the country-level association between the national prevalence of fluoroquinolone resistance in E. coli and the median ciprofloxacin concentration in the country’s rivers. Results: The prevalence of fluoroquinolone resistance in E. coli was positively correlated with the concentration of ciprofloxacin in rivers (ρ = 0.36; p = 0.011; n = 48). Discussion: Steps to reducing the concentrations of fluoroquinolones in rivers may help prevent the emergence of resistance in E. coli and other bacterial species. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

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14 pages, 918 KiB

Open AccessSystematic Review

Prevalence of Antibiotic Resistance in Salmonella Serotypes Concurrently Isolated from the Environment, Animals, and Humans in South Africa: A Systematic Review and Meta-Analysis

by Tsepo Ramatla, Mpho Tawana, ThankGod E. Onyiche, Kgaugelo E. Lekota and Oriel Thekisoe

Antibiotics 2021, 10(12), 1435; https://doi.org/10.3390/antibiotics10121435 - 23 Nov 2021

Cited by 14 | Viewed by 3548

Abstract

One of the main global concerns is the usage and spread of antibiotic resistant Salmonella serovars. The animals, humans, and environmental components interact and contribute to the rapid emergence and spread of antimicrobial resistance, directly or indirectly. Therefore, this study aimed to determine antibiotic resistance (AR) profiles of Salmonella serotypes isolated from the environment, animals, and humans in South Africa by a systematic review and meta-analysis. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were followed to search four databases for studies published from 1980 to 2021, that reported the antibiotic resistance profiles of Salmonella serotypes isolated in South Africa. The AR was screened from 2930 Salmonella serotypes which were isolated from 6842 samples. The Western Cape province had high pooled prevalence estimates (PPE) of Salmonella isolates with AR profiles followed by North West, Gauteng, and Eastern Cape with 94.3%, 75.4%, 59.4%, and 46.2%, respectively. The high PPE and heterogeneity were observed from environmental samples [69.6 (95% CI: 41.7−88.3), Q = 303.643, I² = 98.353, Q-P = 0.045], animals [41.9 (95% CI: 18.5–69.5), Q = 637.355, I² = 98.745, Q-P = 0.577], as well as animals/environment [95.9 (95% CI: 5.4−100), Q = 55.253, I² = 96.380, Q-P = 0.300]. The majority of the salmonella isolates were resistant to sulphonamides (92.0%), enrofloxacin and erythromycin (89.3%), oxytetracycline (77.4%), imipenem (72.6%), tetracycline (67.4%), as well as trimethoprim (52.2%), among the environment, animals, and humans. The level of multidrug-resistance recorded for Salmonella isolates was 28.5% in this review. This study has highlighted the occurrence of AR by Salmonella isolates from animals, humans, and environmental samples in South Africa and this calls for a consolidated “One Health” approach for antimicrobial resistance epidemiological research, as well as the formulation of necessary intervention measures to prevent further spread. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Infectious Diseases: A One Health Perspective)

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