Editorial

4 pages, 191 KiB

Open AccessEditorial

Special Issue “Antimicrobial Resistance: From the Environment to Human Health”

by Carla Viegas and Susana Viegas

Microorganisms 2021, 9(4), 686; https://doi.org/10.3390/microorganisms9040686 - 26 Mar 2021

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Since the 1940s, humans have developed new drugs and consumption has increased significantly in the last 15 years. [...] Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

Research

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16 pages, 3510 KiB

Open AccessArticle

Bacteria Broadly-Resistant to Last Resort Antibiotics Detected in Commercial Chicken Farms

by Jared M. Jochum, Graham A. J. Redweik, Logan C. Ott and Melha Mellata

Microorganisms 2021, 9(1), 141; https://doi.org/10.3390/microorganisms9010141 - 09 Jan 2021

Cited by 12 | Viewed by 3678

Abstract

Resistance to last resort antibiotics in bacteria is an emerging threat to human and animal health. It is important to identify the source of these antimicrobial resistant (AMR) bacteria that are resistant to clinically important antibiotics and evaluate their potential transfer among bacteria. [...] Read more.

Resistance to last resort antibiotics in bacteria is an emerging threat to human and animal health. It is important to identify the source of these antimicrobial resistant (AMR) bacteria that are resistant to clinically important antibiotics and evaluate their potential transfer among bacteria. The objectives of this study were to (i) detect bacteria resistant to colistin, carbapenems, and β-lactams in commercial poultry farms, (ii) characterize phylogenetic and virulence markers of E. coli isolates to potentiate virulence risk, and (iii) assess potential transfer of AMR from these isolates via conjugation. Ceca contents from laying hens from conventional cage (CC) and cage-free (CF) farms at three maturity stages were randomly sampled and screened for extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, carbapenem-resistant Acinetobacter (CRA), and colistin resistant Escherichia coli (CRE) using CHROMagar™ selective media. We found a wide-spread abundance of CRE in both CC and CF hens across all three maturity stages. Extraintestinal pathogenic Escherichia coli phylogenetic groups B2 and D, as well as plasmidic virulence markers iss and iutA, were widely associated with AMR E. coli isolates. ESBL-producing Enterobacteriaceae were uniquely detected in the early lay period of both CC and CF, while multidrug resistant (MDR) Acinetobacter were found in peak and late lay periods of both CC and CF. CRA was detected in CF hens only. bla_CMY was detected in ESBL-producing E. coli in CC and CF and MDR Acinetobacter spp. in CC. Finally, the bla_CMY was shown to be transferrable via an IncK/B plasmid in CC. The presence of MDR to the last-resort antibiotics that are transferable between bacteria in food-producing animals is alarming and warrants studies to develop strategies for their mitigation in the environment. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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16 pages, 2552 KiB

Open AccessArticle

Unearthing Antibiotic Resistance Associated with Disturbance-Induced Permafrost Thaw in Interior Alaska

by Tracie J. Haan and Devin M. Drown

Microorganisms 2021, 9(1), 116; https://doi.org/10.3390/microorganisms9010116 - 06 Jan 2021

Cited by 13 | Viewed by 3794

Abstract

Monitoring antibiotic resistance genes (ARGs) across ecological niches is critical for assessing the impacts distinct microbial communities have on the global spread of resistance. In permafrost-associated soils, climate and human driven disturbances augment near-surface thaw shifting the predominant bacteria that shape the resistome [...] Read more.

Monitoring antibiotic resistance genes (ARGs) across ecological niches is critical for assessing the impacts distinct microbial communities have on the global spread of resistance. In permafrost-associated soils, climate and human driven disturbances augment near-surface thaw shifting the predominant bacteria that shape the resistome in overlying active layer soils. This thaw is of concern in Alaska, because 85% of land is underlain by permafrost, making soils especially vulnerable to disturbances. The goal of this study is to assess how soil disturbance, and the subsequent shift in community composition, will affect the types, abundance, and mobility of ARGs that compose the active layer resistome. We address this goal through the following aims: (1) assess resistance phenotypes through antibiotic susceptibility testing, and (2) analyze types, abundance, and mobility of ARGs through whole genome analyses of bacteria isolated from a disturbance-induced thaw gradient in Interior Alaska. We found a high proportion of isolates resistant to at least one of the antibiotics tested with the highest prevalence of resistance to ampicillin. The abundance of ARGs and proportion of resistant isolates increased with disturbance; however, the number of ARGs per isolate was explained more by phylogeny than isolation site. When compared to a global database of soil bacteria, RefSoil+, our isolates from the same genera had distinct ARGs with a higher proportion on plasmids. These results emphasize the hypothesis that both phylogeny and ecology shape the resistome and suggest that a shift in community composition as a result of disturbance-induced thaw will be reflected in the predominant ARGs comprising the active layer resistome. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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19 pages, 1703 KiB

Open AccessArticle

Detection of Oxazolidinone Resistance Genes and Characterization of Genetic Environments in Enterococci of Swine Origin, Italy

by Simona Fioriti, Gianluca Morroni, Sonia Nina Coccitto, Andrea Brenciani, Alberto Antonelli, Vincenzo Di Pilato, Ilaria Baccani, Simona Pollini, Lucilla Cucco, Alessandra Morelli, Marta Paniccià, Chiara Francesca Magistrali, Gian Maria Rossolini and Eleonora Giovanetti

Microorganisms 2020, 8(12), 2021; https://doi.org/10.3390/microorganisms8122021 - 17 Dec 2020

Cited by 34 | Viewed by 2851

Abstract

One hundred forty-five florfenicol-resistant enterococci, isolated from swine fecal samples collected from 76 pig farms, were investigated for the presence of optrA, cfr, and poxtA genes by PCR. Thirty florfenicol-resistant Enterococcus isolates had at least one linezolid resistance gene. optrA was [...] Read more.

One hundred forty-five florfenicol-resistant enterococci, isolated from swine fecal samples collected from 76 pig farms, were investigated for the presence of optrA, cfr, and poxtA genes by PCR. Thirty florfenicol-resistant Enterococcus isolates had at least one linezolid resistance gene. optrA was found to be the most widespread linezolid resistance gene (23/30), while cfr and poxtA were detected in 6/30 and 7/30 enterococcal isolates, respectively. WGS analysis also showed the presence of the cfr(D) gene in Enterococcus faecalis (n = 2 isolates) and in Enterococcus avium (n = 1 isolate). The linezolid resistance genes hybridized both on chromosome and plasmids ranging from ~25 to ~240 kb. Twelve isolates were able to transfer linezolid resistance genes to enterococci recipient. WGS analysis displayed a great variability of optrA genetic contexts identical or related to transposons (Tn6628 and Tn6674), plasmids (pE035 and pWo27-9), and chromosomal regions. cfr environments showed identities with Tn6644-like transposon and a region from p12-2300 plasmid; cfr(D) genetic contexts were related to the corresponding region of the plasmid 4 of Enterococcus faecium E8014; poxtA was always found on Tn6657. Circular forms were obtained only for optrA- and poxtA-carrying genetic contexts. Clonality analysis revealed the presence of E. faecalis (ST16, ST27, ST476, and ST585) and E. faecium (ST21) clones previously isolated from humans. These results demonstrate a dissemination of linezolid resistance genes in enterococci of swine origin in Central Italy and confirm the spread of linezolid resistance in animal settings. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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16 pages, 7282 KiB

Open AccessArticle

Comparative Pathogenomics of Aeromonas veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone

by Yogandree Ramsamy, Koleka P. Mlisana, Daniel G. Amoako, Akebe Luther King Abia, Mushal Allam, Arshad Ismail, Ravesh Singh and Sabiha Y. Essack

Microorganisms 2020, 8(12), 2008; https://doi.org/10.3390/microorganisms8122008 - 16 Dec 2020

Cited by 7 | Viewed by 2669

Abstract

The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The [...] Read more.

The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed. All the isolates had similar resistance phenotypes, which corroborated their chromosomally mediated resistome (bla_CPHA₃ and bla_OXA-₁₂) and belonged to a novel sequence type, ST657 (a satellite clone). Isolates in the same sub-clades clustered according to their clonal lineages and host. Mobilome analysis revealed the presence of chromosome-borne insertion sequence families. The estimated pathogenicity score (P_score ≈ 0.60) indicated their potential pathogenicity in humans. Furthermore, these isolates carried several virulence factors (adherence factors, toxins, and immune evasion), in different permutations and combinations, indicating a differential ability to establish infection. Phylogenomic and metadata analyses revealed a predilection for water environments and aquatic animals, with more recent reports in humans and food animals across geographies, making A. veronii a potential One Health indicator bacterium. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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18 pages, 1989 KiB

Open AccessArticle

Shared Extended-Spectrum β-Lactamase-Producing Salmonella Serovars between Agricultural and Aquatic Environments Revealed through invA Amplicon Sequencing

by Cecilia Mahlatse Raseala, Mutshiene Deogratias Ekwanzala and Maggy Ndombo Benteke Momba

Microorganisms 2020, 8(12), 1898; https://doi.org/10.3390/microorganisms8121898 - 30 Nov 2020

Cited by 9 | Viewed by 2191

Abstract

The presence of antibiotic-resistant Salmonella spp. in the environment is of great public health interest, worldwide. Furthermore, its extended-spectrum β-lactamase (ESBL)-producing strains constitute an emerging global health concern due to their limited treatment options in hospital. Therefore, this study aimed at characterising and [...] Read more.

The presence of antibiotic-resistant Salmonella spp. in the environment is of great public health interest, worldwide. Furthermore, its extended-spectrum β-lactamase (ESBL)-producing strains constitute an emerging global health concern due to their limited treatment options in hospital. Therefore, this study aimed at characterising and tracking nonresistant and ESBL–producing Salmonella spp. from agricultural settings to nearby water sources highlighting their antibiotic resistance genes (ARG) and virulence factor (VF) distribution using a combination of both culture-dependent and independent methods. Furthermore, this study investigated the diversity and shared serovars among sampled matrices using amplicon sequencing of the invasion gene A (invA) of Salmonella spp. The results showed that soil had the highest prevalence of Salmonella spp. (62.5%, 65/104) and ESBL-producing Salmonella (34.6%, 36/104). For typed ARG, the most commonly detected gene was bla_OXA with 75% (30/40), followed by bla_CTX-M 67.5% (27/40)_,bla_TEM 40% (16/40) and sul1 30% (12/40) gene; bla_SHV gene was not detected in isolated ESBL-producing Salmonella spp. For VF, the most detected gene was invA (96.9%, 38/40), followed by spaM (17.5%, 7/40), spiC (40%, 16/40), orfL (32.5%, 13/40), misL 32.5% (13/40) and pipD 32.5 (13/40). For diversity analysis, soil, manure, irrigation water and nearby freshwater revealed 81, 68, 12 and 9 serovars, respectively. Soil, manure, irrigation water and freshwater stream samples shared five serovars, which indicated circulation of ESBL-producing Salmonella spp. within the agricultural environment and nearby water sources. Soil is therefore identified as one of the major reservoirs of ESBL-producing Salmonella spp. It is concluded that agricultural environment contamination may have a direct relationship with the presence of antibiotic-producing Salmonella in freshwater streams. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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18 pages, 1563 KiB

Open AccessArticle

Settleable Dust and Bioburden in Portuguese Dwellings

by Carla Viegas, Marta Dias, Beatriz Almeida, Estela Vicente, Liliana Aranha Caetano, Elisabete Carolino and Célia Alves

Microorganisms 2020, 8(11), 1799; https://doi.org/10.3390/microorganisms8111799 - 16 Nov 2020

Cited by 10 | Viewed by 2224

Abstract

Monitoring campaigns in several buildings have shown that occupants exposed to contaminated indoor air generally exhibit diverse health symptoms. This study intends to assess settleable dust loading rates and bioburden in Portuguese dwellings by passive sampling onto quartz fiber filters and electrostatic dust [...] Read more.

Monitoring campaigns in several buildings have shown that occupants exposed to contaminated indoor air generally exhibit diverse health symptoms. This study intends to assess settleable dust loading rates and bioburden in Portuguese dwellings by passive sampling onto quartz fiber filters and electrostatic dust cloths (EDCs), respectively. Settled dust collected by EDCs was analyzed by culture-based methods (including azole-resistance screening) and qPCR, targeting four different toxigenic Aspergillus sections (Flavi, Fumigati, Circumdati, and Nidulantes). Dust loading rates and bioburden showed higher variability in the summer season. In both seasons, Penicillium sp. was the one with the highest prevalence (59.1% winter; 58.1% summer), followed by Aspergillus sp. in winter (13.0%). Fungal contamination increased in the winter period, while bacterial counts decreased. Aspergillus sections Circumdati and Nidulantes, detected in voriconazole supplemented media, and Aspergillus sections Fumigati and Nidulantes, detected by molecular tools, were found in the winter samples. This study reinforces the importance of applying: (a) Passive sampling methods in campaigns in dwellings; (b) two different culture media (MEA and DG18) to assess fungi; (c) in parallel, molecular tools targeting the most suitable indicators of fungal contamination; and (d) azole resistance screening to unveil azole resistance detection in fungal species. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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18 pages, 1705 KiB

Open AccessArticle

Long-Term Persistence of bla_CTX-M-15 in Soil and Lettuce after Introducing Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli via Manure or Water

by Maria-Theresia Gekenidis, Serena Rigotti, Jörg Hummerjohann, Fiona Walsh and David Drissner

Microorganisms 2020, 8(11), 1646; https://doi.org/10.3390/microorganisms8111646 - 23 Oct 2020

Cited by 17 | Viewed by 2780

Abstract

The number of environmental antibiotic-resistant bacteria (ARB) has increased dramatically since the start of antibiotic mass production for broad bacterial infection treatment in 1944. Nowadays, ARB and their resistance-determining genes (ARGs) are readily detected in all environments, including the human food chain. A [...] Read more.

The number of environmental antibiotic-resistant bacteria (ARB) has increased dramatically since the start of antibiotic mass production for broad bacterial infection treatment in 1944. Nowadays, ARB and their resistance-determining genes (ARGs) are readily detected in all environments, including the human food chain. A highly relevant food group in this context is fresh produce, frequent raw consumption of which facilitates direct transfer of ARB and ARGs to the consumer. Here, we investigate the persistence of an extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) pEK499 and its clinically most important ARG (bla_CTX-M-15), after introduction via irrigation water or manure into a lettuce-growing system. Culturable ESBL-producing E. coli persisted longest in soil and when introduced via manure (until 9 weeks after introduction), while being undetectable on lettuce beyond day 7. In contrast, qPCR detection of bla_CTX-M-15 was much more frequent: introduction via water significantly increased bla_CTX-M-15 on lettuce until week 4, as opposed to manure, which affected the soil in the long-term (9 weeks) while leading to bla_CTX-M-15 detection on lettuce until day 7 only. Our findings demonstrate long-term persistence of undesired ARB and ARG after their introduction via both irrigation and amendment. Such an understanding of the persistence kinetics of an ESBL-producing E. coli and plasmid-encoded bla_CTX-M-15 aids the determination of critical actions in order to mitigate their transfer to the consumer. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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9 pages, 668 KiB

Open AccessArticle

Antibiotic-Resistant Escherichia coli and Sequence Type 131 in Fecal Colonization in Dogs in Taiwan

by Jenn-Wei Chen, Han Hsiang Huang, Szu-Min Chang, Joy Scaria, Yu-Lung Chiu, Chih-Ming Chen, Wen-Chien Ko and Jiun-Ling Wang

Microorganisms 2020, 8(9), 1439; https://doi.org/10.3390/microorganisms8091439 - 20 Sep 2020

Cited by 14 | Viewed by 2653

Abstract

Background: Most drug-resistant Escherichia coli isolates in dogs come from diseased dogs. Prior to this study, the prevalence and risk factors of fecal carriage drug-resistant E. coli and epidemic clone sequence type (ST) 131 (including subtypes) isolates in dogs were unknown. Methods: Rectal [...] Read more.

Background: Most drug-resistant Escherichia coli isolates in dogs come from diseased dogs. Prior to this study, the prevalence and risk factors of fecal carriage drug-resistant E. coli and epidemic clone sequence type (ST) 131 (including subtypes) isolates in dogs were unknown. Methods: Rectal swabs were used for E. coli isolation from 299 non-infectious dogs in a veterinary teaching hospital in Taiwan. Antibiotic resistance and multiplex PCR analyses of E. coli for major STs were performed. Result: There were 43.1% cefazolin-resistant, 22.1% fluoroquinolone-resistant, and 9.4% extended-spectrum beta-lactamase-producing E. coli in our cohort. In the phylogenetic study, B2 was the predominant group (30.1%). The cefazolin-resistant group and ciprofloxacin-resistant group had greater antibiotic exposure in the last 14 days (p < 0.05). The age, sex, and dietary habits of the antibiotic-resistant and -susceptible groups were similar. In the seven isolates of ST131 in fecal colonization, the most predominant subtypes were FimH41 and FimH22. Conclusion: Recent antibiotic exposure was related to the fecal carriage of antibiotic-resistant E. coli isolates. Three major subtypes (FimH41, H22, and H30) of ST131 can thus be found in fecal carriage in dogs in Taiwan. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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15 pages, 1483 KiB

Open AccessArticle

Transferable Extended-Spectrum β-Lactamase (ESBL) Plasmids in Enterobacteriaceae from Irrigation Water

by Maria-Theresia Gekenidis, Anita Kläui, Kornelia Smalla and David Drissner

Microorganisms 2020, 8(7), 978; https://doi.org/10.3390/microorganisms8070978 - 30 Jun 2020

Cited by 17 | Viewed by 3986

Abstract

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are classified as serious threats to human health by the U.S. Centers for Disease Control and Prevention. Water used for irrigation of fresh produce can transmit such resistant bacteria directly to edible plant parts. We screened ESBL-producing Escherichia coli [...] Read more.

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are classified as serious threats to human health by the U.S. Centers for Disease Control and Prevention. Water used for irrigation of fresh produce can transmit such resistant bacteria directly to edible plant parts. We screened ESBL-producing Escherichia coli, Enterobacter cloacae, and Citrobacter freundii isolated from irrigation water for their potential to transmit resistance to antibiotic-susceptible E. coli. All strains were genome-sequenced and tested in vitro for transmission of resistance to third-generation cephalosporins on solid agar as well as in liquid culture. Of the 19 screened isolates, five ESBL-producing E. coli were able to transfer resistance with different efficiency to susceptible recipient E. coli. Transconjugant strains were sequenced for detection of transferred antibiotic resistance genes (ARGs) and compared to the known ARG pattern of their respective donors. Additionally, phenotypic resistance patterns were obtained for both transconjugant and corresponding donor strains, confirming ESBL-producing phenotypes of all obtained transconjugants. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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22 pages, 980 KiB

Open AccessArticle

A One Health Comparative Assessment of Antimicrobial Resistance in Generic and Extended-Spectrum Cephalosporin-Resistant Escherichia coli from Beef Production, Sewage and Clinical Settings

by Emelia H. Adator, Claudia Narvaez-Bravo, Rahat Zaheer, Shaun R. Cook, Lisa Tymensen, Sherry J. Hannon, Calvin W. Booker, Deirdre Church, Ron R. Read and Tim A. McAllister

Microorganisms 2020, 8(6), 885; https://doi.org/10.3390/microorganisms8060885 - 11 Jun 2020

Cited by 16 | Viewed by 3994

Abstract

This study aimed to compare antimicrobial resistance (AMR) in extended-spectrum cephalosporin-resistant and generic Escherichia coli from a One Health continuum of the beef production system in Alberta, Canada. A total of 705 extended-spectrum cephalosporin-resistant E. coli (ESC^r) were obtained from: cattle [...] Read more.

This study aimed to compare antimicrobial resistance (AMR) in extended-spectrum cephalosporin-resistant and generic Escherichia coli from a One Health continuum of the beef production system in Alberta, Canada. A total of 705 extended-spectrum cephalosporin-resistant E. coli (ESC^r) were obtained from: cattle feces (CFeces, n = 382), catch basins (CBasins, n = 137), surrounding streams (SStreams, n = 59), beef processing plants (BProcessing, n = 4), municipal sewage (MSewage; n = 98) and human clinical specimens (CHumans, n = 25). Generic isolates (663) included: CFeces (n = 142), CBasins (n = 185), SStreams (n = 81), BProcessing (n = 159) and MSewage (n = 96). All isolates were screened for antimicrobial susceptibility to 9 antimicrobials and two clavulanic acid combinations. In ESC^r, oxytetracycline (87.7%), ampicillin (84.4%) and streptomycin (73.8%) resistance phenotypes were the most common, with source influencing AMR prevalence (p < 0.001). In generic E. coli, oxytetracycline (51.1%), streptomycin (22.6%), ampicillin (22.5%) and sulfisoxazole (14.3%) resistance were most common. Overall, 88.8% of ESC^r, and 26.7% of generic isolates exhibited multi-drug resistance (MDR). MDR in ESC^r was high from all sources: CFeces (97.1%), MSewage (96.9%), CHumans (96%), BProcessing (100%), CBasins (70.5%) and SStreams (61.4%). MDR in generic E. coli was lower with CFeces (45.1%), CBasins (34.6%), SStreams (23.5%), MSewage (13.6%) and BProcessing (10.7%). ESBL phenotypes were confirmed in 24.7% (n = 174) ESC^r and 0.6% of generic E. coli. Prevalence of bla genes in ESC^r were bla_CTXM (30.1%), bla_CTXM-1 (21.6%), bla_TEM (20%), bla_CTXM-9 (7.9%), bla_OXA (3.0%), bla_CTXM-2 (6.4%), bla_SHV (1.4%) and AmpC β-lactamase bla_CMY (81.3%). The lower AMR in ESC^r from SStreams and BProcessing and higher AMR in CHumans and CFeces likely reflects antimicrobial use in these environments. Although MDR levels were higher in ESC^r as compared to generic E. coli, AMR to the same antimicrobials ranked high in both ESC^r and generic E. coli sub-populations. This suggests that both sub-populations reflect similar AMR trends and are equally useful for AMR surveillance. Considering that MDR ESC^r MSewage isolates were obtained without enrichment, while those from CFeces were obtained with enrichment, MSewage may serve as a hot spot for MDR emergence and dissemination. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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15 pages, 1707 KiB

Open AccessArticle

A Clinical Perspective on the Antimicrobial Resistance Spectrum of Uropathogens in a Romanian Male Population

by Călin Bogdan Chibelean, Răzvan-Cosmin Petca, Cristian Mareș, Răzvan-Ionuț Popescu, Barabás Enikő, Claudia Mehedințu and Aida Petca

Microorganisms 2020, 8(6), 848; https://doi.org/10.3390/microorganisms8060848 - 05 Jun 2020

Cited by 19 | Viewed by 2828

Abstract

Considering urinary tract infections (UTIs), a significant public health problem with negligible recent research, especially on the male eastern European population, we aimed to determine the antimicrobial resistance rates of uropathogens for the most commonly used antibiotics in urological practice in our country. [...] Read more.

Considering urinary tract infections (UTIs), a significant public health problem with negligible recent research, especially on the male eastern European population, we aimed to determine the antimicrobial resistance rates of uropathogens for the most commonly used antibiotics in urological practice in our country. We conducted a multicenter retrospective study in two different teaching hospitals in Romania, analyzing urine samples from 7719 patients to determine the frequency of incriminating pathogens and their resistance to different antibiotics, in a comparative approach. We determined Escherichia coli (35.98%) to be the most common pathogen with the highest sensitivity to amikacin (S = 91.72%), meropenem (S = 97.17%) and fosfomycin (S = 86.60%) and important resistance to amoxicillin-clavulanic ac. (R = 28.03%) and levofloxacin (R = 37.69%), followed by Klebsiella spp. (22.98%) with the highest sensitivity to amikacin (S = 78.04%) and meropenem (S = 81.35%) and important resistance to amoxicillin-clavulanic ac. (R = 65.58%) and levofloxacin (R = 45.36%); the most frequent Gram-positive pathogen was Enterococcus spp. (19.73%) with the highest sensitivity for vancomycin (S = 93.75%) and fosfomycin (S = 87.5%) and considerable resistance to penicillin (R = 33.52%) and levofloxacin (R = 42.04%). The findings are an important tool in managing UTIs and should be acknowledged as reference research not only for clinicians from Romania but for all physicians treating male UTIs. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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18 pages, 1825 KiB

Open AccessArticle

Antimicrobial Resistance Traits of Escherichia coli Isolated from Dairy Manure and Freshwater Ecosystems Are Similar to One Another but Differ from Associated Clinical Isolates

by Rachelle E. Beattie, Ellen Bakke, Nicholas Konopek, Rebecca Thill, Erik Munson and Krassimira R. Hristova

Microorganisms 2020, 8(5), 747; https://doi.org/10.3390/microorganisms8050747 - 16 May 2020

Cited by 8 | Viewed by 2403

Abstract

Antimicrobial resistance (AMR) is a prevalent global health problem across human and veterinary medicine. The One Health approach to AMR is necessary to mitigate transmission between sources of resistance and decrease the spread of resistant bacteria among humans, animals, and the environment. Our [...] Read more.

Antimicrobial resistance (AMR) is a prevalent global health problem across human and veterinary medicine. The One Health approach to AMR is necessary to mitigate transmission between sources of resistance and decrease the spread of resistant bacteria among humans, animals, and the environment. Our primary goal was to identify associations in resistance traits between Escherichia coli isolated from clinical (n = 103), dairy manure (n = 65), and freshwater ecosystem (n = 64) environments within the same geographic location and timeframe. Clinical E. coli isolates showed the most phenotypic resistance (47.5%), followed by environmental isolates (15.6%) and manure isolates (7.7%), with the most common resistances to ampicillin, ampicillin-sulbactam, and cefotaxime antibiotics. An isolate subset was screened for extended spectrum beta-lactamase (ESBL) production resulting in the identification of 35 ESBL producers. The most common ESBL gene identified was bla_TEM-1. Additionally, we found nine different plasmid replicon types including IncFIA-FIB, which were frequently associated with ESBL producer isolates. Molecular phylotyping revealed a significant portion of clinical E. coli were associated with phylotype B2, whereas manure and environmental isolates were more diverse. Manure and environmental isolates were significantly different from clinical isolates based on analyzed traits, suggesting more transmission occurs between these two sources in the sampled environment. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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13 pages, 2060 KiB

Open AccessArticle

The Aquatic Ecosystem, a Good Environment for the Horizontal Transfer of Antimicrobial Resistance and Virulence-Associated Factors Among Extended Spectrum β-lactamases Producing E. coli

by Lara Pérez-Etayo, David González and Ana Isabel Vitas

Microorganisms 2020, 8(4), 568; https://doi.org/10.3390/microorganisms8040568 - 15 Apr 2020

Cited by 9 | Viewed by 2740

Abstract

One of the main public health problems nowadays is the increase of antimicrobial resistance, both in the hospital environment and outside it (animal environment, food and aquatic ecosystems, among others). It is necessary to investigate the virulence-associated factors and the ability of horizontal [...] Read more.

One of the main public health problems nowadays is the increase of antimicrobial resistance, both in the hospital environment and outside it (animal environment, food and aquatic ecosystems, among others). It is necessary to investigate the virulence-associated factors and the ability of horizontal gene transfer among bacteria for a better understanding of the pathogenicity and the mechanisms of dissemination of resistant bacteria. Therefore, the objective of this work was to detect several virulence factors genes (fimA, papC, papG III, cnf1, hlyA and aer) and to determine the conjugative capacity in a wide collection of extended-spectrum β-lactamases-producing E. coli isolated from different sources (human, food, farms, rivers, and wastewater treatment plants). Regarding virulence genes, fimA, papC, and aer were distributed throughout all the studied environments, papG III was mostly related to clinical strains and wastewater is a route of dissemination for cnf1 and hlyA. Strains isolated from aquatic environments showed an average conjugation frequencies of 1.15 × 10⁻¹ ± 5 × 10⁻¹, being significantly higher than those observed in strains isolated from farms and food (p < 0.05), with frequencies of 1.53 × 10⁻⁴ ± 2.85 × 10⁻⁴ and 9.61 × 10⁻⁴ ± 1.96 × 10⁻³, respectively. The reported data suggest the importance that the aquatic environment (especially WWTPs) acquires for the exchange of genes and the dispersion of resistance. Therefore, specific surveillance programs of AMR indicators in wastewaters from animal or human origin are needed, in order to apply sanitation measures to reduce the burden of resistant bacteria arriving to risky environments as WWTPs. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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19 pages, 1818 KiB

Open AccessArticle

The Porcine Nasal Microbiota with Particular Attention to Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Germany—A Culturomic Approach

by Andreas Schlattmann, Knut von Lützau, Ursula Kaspar and Karsten Becker

Microorganisms 2020, 8(4), 514; https://doi.org/10.3390/microorganisms8040514 - 04 Apr 2020

Cited by 7 | Viewed by 3335

Abstract

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) remains a serious public health threat. Porcine nasal cavities are predominant habitats of LA-MRSA. Hence, components of their microbiota might be of interest as putative antagonistically acting competitors. Here, an extensive culturomics approach has been applied including 27 [...] Read more.

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) remains a serious public health threat. Porcine nasal cavities are predominant habitats of LA-MRSA. Hence, components of their microbiota might be of interest as putative antagonistically acting competitors. Here, an extensive culturomics approach has been applied including 27 healthy pigs from seven different farms; five were treated with antibiotics prior to sampling. Overall, 314 different species with standing in nomenclature and 51 isolates representing novel bacterial taxa were detected. Staphylococcus aureus was isolated from pigs on all seven farms sampled, comprising ten different spa types with t899 (n = 15, 29.4%) and t337 (n = 10, 19.6%) being most frequently isolated. Twenty-six MRSA (mostly t899) were detected on five out of the seven farms. Positive correlations between MRSA colonization and age and colonization with Streptococcus hyovaginalis, and a negative correlation between colonization with MRSA and Citrobacter spp. were found (p < 0.05). Of 209 non-S. aureus members of the Staphylococcaceae family, 25 isolates (12.0%) from three out of the seven farms exhibited methicillin resistance, including two Macrococcus goetzii isolates carrying the mecB gene. Among 125 Enterobacterales, none tested positive for extended-spectrum beta-lactamase (ESBL) and carbapenemase production. The high frequency of methicillin-resistant staphylococci supports the need for enhanced efforts within the “One Health” concept to manage the antibiotic resistance crisis in the human and veterinary medicine sector. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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21 pages, 1225 KiB

Open AccessArticle

Occupational Exposures to Organic Dust in Irish Bakeries and a Pizzeria Restaurant

by Carla Viegas, Gerard T. A. Fleming, Abdul Kadir, Beatriz Almeida, Liliana Aranha Caetano, Anita Quintal Gomes, Magdalena Twarużek, Robert Kosicki, Susana Viegas and Ann Marie Coggins

Microorganisms 2020, 8(1), 118; https://doi.org/10.3390/microorganisms8010118 - 15 Jan 2020

Cited by 23 | Viewed by 4123

Abstract

For decades, occupational exposure to flour dust has been linked to a range of respiratory diseases, including occupational asthma, thought to result from exposure to fungi present in the flour. Antifungal resistance is of increasing prevalence in clinical settings, and the role of [...] Read more.

For decades, occupational exposure to flour dust has been linked to a range of respiratory diseases, including occupational asthma, thought to result from exposure to fungi present in the flour. Antifungal resistance is of increasing prevalence in clinical settings, and the role of occupational and environmental exposures, particularly for specific fungal species, is of concern. Occupational exposure to flour dust can occur in a range of occupational settings, however, few studies have focused on restaurant workers. The objective of this study was to measure occupational exposure to flour and microbial contamination, including azole resistance screening, in two small commercial bakeries and in a pizzeria. Personal full shift inhalable dust measurements were collected from workers, and were analyzed for inhalable dust and fungi, bacteria, azole resistance, and mycotoxins. Samples of settled dust were collected, and electrostatic dust cloths (EDC) were deployed and analyzed for microbial contamination, including azole resistance screening, and mycotoxins. Geometric mean exposures of 6.5 mg m⁻³ were calculated for inhalable dust, however, exposures of up to 18.30 mg m⁻³ were measured—70% of personal exposure measurements exceeded the occupational exposure limit for flour dust of 1.0 mg m⁻³. The air and EDC fungal counts were similar to those reported in previous studies for similar occupational environments. The fungi were dominated by Penicillium genera, however Aspergillus genera, including Fumigati and Flavi sections, were observed using culture-based methods, and the Fumigati section was also observed by molecular tools. Both Aspergillus sections were identified on the azole resistance screening. Mycotoxins were also detected in the settled dust samples, dominated by deoxynivalenol (DON). The role of environmental exposure in both the development of antimicrobial resistance and the total mycotoxin body burden is a growing concern; therefore, the presence of azole-resistant fungi and mycotoxin contamination, although low in magnitude, is of concern and warrants further investigation. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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16 pages, 2431 KiB

Open AccessArticle

Insights into Antagonistic Interactions of Multidrug Resistant Bacteria in Mangrove Sediments from the South Indian State of Kerala

by Madangchanok Imchen, Ravali Krishna Vennapu, Preetam Ghosh and Ranjith Kumavath

Microorganisms 2019, 7(12), 678; https://doi.org/10.3390/microorganisms7120678 - 11 Dec 2019

Cited by 14 | Viewed by 5485

Abstract

Antibiotic resistance is a global issue which is magnified by interspecies horizontal gene transfer. Understanding antibiotic resistance in bacteria in a natural setting is crucial to check whether they are multidrug resistant (MDR) and possibly avoid outbreaks. In this study, we have isolated [...] Read more.

Antibiotic resistance is a global issue which is magnified by interspecies horizontal gene transfer. Understanding antibiotic resistance in bacteria in a natural setting is crucial to check whether they are multidrug resistant (MDR) and possibly avoid outbreaks. In this study, we have isolated several antibiotic-resistant bacteria (ARB) (n = 128) from the mangroves in Kerala, India. ARBs were distributed based on antibiotics (p = 1.6 × 10⁻⁵). The 16S rRNA gene characterization revealed dominance by Bacillaceae (45%), Planococcaceae (22.5%), and Enterobacteriaceae (17.5%). A high proportion of the isolates were MDR (75%) with maximum resistance to methicillin (70%). Four isolates affiliated to plant-growth promoters, probiotics, food, and human pathogens were resistant to all antibiotics indicating the seriousness and prevalence of MDR. A significant correlation (R = 0.66; p = 2.5 × 10⁻⁶) was observed between MDR and biofilm formation. Antagonist activity was observed in 62.5% isolates. Gram-positive isolates were more susceptible to antagonism (75.86%) than gram-negative (36.36%) isolates. Antagonism interactions against gram-negative isolates were lower (9.42%) when compared to gram-positive isolates (89.85%). Such strong antagonist activity can be harnessed for inspection of novel antimicrobial mechanisms and drugs. Our study shows that MDR with strong biofilm formation is prevalent in natural habitat and if acquired by deadly pathogens may create havoc in public health. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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15 pages, 1801 KiB

Open AccessReview

Mitochondria-Mediated Azole Drug Resistance and Fungal Pathogenicity: Opportunities for Therapeutic Development

by Jinxing Song, Jingwen Zhou, Lei Zhang and Rongpeng Li

Microorganisms 2020, 8(10), 1574; https://doi.org/10.3390/microorganisms8101574 - 13 Oct 2020

Cited by 24 | Viewed by 3637

Abstract

In recent years, the role of mitochondria in pathogenic fungi in terms of azole resistance and fungal pathogenicity has been a rapidly developing field. In this review, we describe the molecular mechanisms by which mitochondria are involved in regulating azole resistance and fungal [...] Read more.

In recent years, the role of mitochondria in pathogenic fungi in terms of azole resistance and fungal pathogenicity has been a rapidly developing field. In this review, we describe the molecular mechanisms by which mitochondria are involved in regulating azole resistance and fungal pathogenicity. Mitochondrial function is involved in the regulation of drug efflux pumps at the transcriptional and posttranslational levels. On the one hand, defects in mitochondrial function can serve as the signal leading to activation of calcium signaling and the pleiotropic drug resistance pathway and, therefore, can globally upregulate the expression of drug efflux pump genes, leading to azole drug resistance. On the other hand, mitochondria also contribute to azole resistance through modulation of drug efflux pump localization and activity. Mitochondria further contribute to azole resistance through participating in iron homeostasis and lipid biosynthesis. Additionally, mitochondrial dynamics play an important role in azole resistance. Meanwhile, mitochondrial morphology is important for fungal virulence, playing roles in growth in stressful conditions in a host. Furthermore, there is a close link between mitochondrial respiration and fungal virulence, and mitochondrial respiration plays an important role in morphogenetic transition, hypoxia adaptation, and cell wall biosynthesis. Finally, we discuss the possibility for targeting mitochondrial factors for the development of antifungal therapies. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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16 pages, 1648 KiB

Open AccessReview

Correlation between Exogenous Compounds and the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes

by Yuan Liu, Ziwen Tong, Jingru Shi, Yuqian Jia, Kangni Yang and Zhiqiang Wang

Microorganisms 2020, 8(8), 1211; https://doi.org/10.3390/microorganisms8081211 - 08 Aug 2020

Cited by 39 | Viewed by 12315

Abstract

The global spread of antibiotic resistance has posed a serious threat to public healthcare and undermined decades of progress made in the fight against bacterial infections. It has been demonstrated that the lack of novel effective antibiotics and rapid spread of antibiotic resistance [...] Read more.

The global spread of antibiotic resistance has posed a serious threat to public healthcare and undermined decades of progress made in the fight against bacterial infections. It has been demonstrated that the lack of novel effective antibiotics and rapid spread of antibiotic resistance genes via horizontal transfer in the ecosystem are mainly responsible for this crisis. Notably, plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) is recognized as the most dominant dissemination pathway of ARGs in humans, animals and environmental settings. Antibiotic selective pressure has always been regarded as one of the crucial contributors to promoting the dissemination of antibiotic resistance through horizontal gene transfer (HGT). However, the roles of exogenous compounds and particularly non-antibiotic drugs in the spread of ARGs are still underappreciated. In this review, we first summarize the major pathways of HGT in bacteria, including conjugation, transformation, transduction and vesiduction. Subsequently, an overview of these compounds capable of promoting the HGT is presented, which guides to the formulation of more reasonable dosing regimens and drug residue standards in clinical practice. By contrast, these compounds that display an inhibition effect on HGT are also highlighted, which provides a unique strategy to minimize the spread of ARGs. Lastly, we discuss the implementations and challenges in bringing these HGT inhibitors into clinical trials. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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40 pages, 665 KiB

Open AccessReview

Antibiotic Resistance Profiles, Molecular Mechanisms and Innovative Treatment Strategies of Acinetobacter baumannii

by Corneliu Ovidiu Vrancianu, Irina Gheorghe, Ilda Barbu Czobor and Mariana Carmen Chifiriuc

Microorganisms 2020, 8(6), 935; https://doi.org/10.3390/microorganisms8060935 - 21 Jun 2020

Cited by 98 | Viewed by 11422

Abstract

Antibiotic resistance is one of the biggest challenges for the clinical sector and industry, environment and societal development. One of the most important pathogens responsible for severe nosocomial infections is Acinetobacter baumannii, a Gram-negative bacterium from the Moraxellaceae family, due to its [...] Read more.

Antibiotic resistance is one of the biggest challenges for the clinical sector and industry, environment and societal development. One of the most important pathogens responsible for severe nosocomial infections is Acinetobacter baumannii, a Gram-negative bacterium from the Moraxellaceae family, due to its various resistance mechanisms, such as the β-lactamases production, efflux pumps, decreased membrane permeability and altered target site of the antibiotic. The enormous adaptive capacity of A. baumannii and the acquisition and transfer of antibiotic resistance determinants contribute to the ineffectiveness of most current therapeutic strategies, including last-line or combined antibiotic therapy. In this review, we will present an update of the antibiotic resistance profiles and underlying mechanisms in A. baumannii and the current progress in developing innovative strategies for combating multidrug-resistant A. baumannii (MDRAB) infections. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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