A Decade-Long Commitment to Antimicrobial Resistance Surveillance in Portugal

Antimicrobial resistance profiles of Escherichia coli isolated from laying hens in Zambia: implications and significance on one health

Background

Antimicrobial resistance (AMR) has been deepening in the layer poultry sector in Zambia partly due to the inappropriate use of antimicrobials. Escherichia coli (E. coli), a commensal and zoonotic bacterium, can potentially be a source of AMR.

Objectives

This study assessed the phenotypic AMR profiles of E. coli isolated from the apparent health-laying hens in Lusaka and Copperbelt provinces of Zambia.

Methods

A cross-sectional study was conducted between September 2020 and April 2021 in which 365 cloacal swabs were collected from 77-layer farms based in Lusaka and Copperbelt provinces of Zambia. E. coli isolation and identification were done using cultural and biochemical properties and confirmed using the 16S rRNA gene sequencing. Antimicrobial susceptibility testing (AST) was done using the Kirby-Bauer disc-diffusion method. Data analysis was done using WHONET 2020 and Stata v.16.1.

Results

Of the 365 samples, E. coli was isolated from 92.9% (n = 339). The AMR was detected in 96.5% (n = 327) of the isolates, of which 64.6% (n = 219) were multidrug-resistant (MDR). E. coli was highly resistant to tetracycline (54.6%) and ampicillin (54%) but showed low resistance to meropenem (0.9%), ceftazidime (6.2%) and chloramphenicol (8.8%).

Conclusion

This study found a high prevalence of E. coli resistant to some commonly used antibiotics in poultry, which is a public health concern because of the potential contamination of eggs and layers of chicken meat that enter the food chain. Urgent attention is needed, including strengthening antimicrobial stewardship and surveillance programmes in layer poultry production in Zambia.

Phenotypic antimicrobial resistance (AMR) of avian pathogenic Escherichia coli (APEC) from broiler breeder flocks between 2009 and 2018

Colibacillosis is one of the most important diseases in poultry production. The use of antimicrobials remains a therapeutic cornerstone for avian pathogenic E. coli (APEC), thereby contributing to the development of antimicrobial resistance (AMR). The aim of this study was to characterize AMR in broiler breeder flocks reared under commercial conditions. Data covering ten years, from 2009 to 2018, were used to evaluate the phenotypic AMR of 264 APEC obtained from 158 broiler breeder flocks of a large company in Portugal. The APEC isolates were tested against eleven antimicrobials by the Kirby-Bauer disk diffusion test. The annual proportion of AMR was calculated by dividing the number of APEC with phenotypic resistance by the total number of APEC isolated that year. Similarly, the overall AMR of the whole period was calculated. The relationship of antimicrobial resistance with time (years) was investigated with a generalized linear model using logistic regression. The overall AMR of the 10-year period was: amoxicillin 78%, ampicillin 73.5%, tetracycline 63.3%, doxycycline 56.4%, apramycin 34.5%, neomycin 68.2%, enrofloxacine 32.6%, flumequine 39.4%, co-trimoxazole 47.7%, florfenicol 46.6% and lincospectin 66.3%. Over time, a significant decrease in AMR was observed for amoxicillin and ampicillin, neomycin, flumequine, co-trimoxazole, florfenicol and lincospectin. Multidrug resistance (MDR) decreased from 100% in 2009 to 48% in 2018. Only 7 (2.7%) APEC strains were fully susceptible to all tested antimicrobials. The decrease over time of AMR in APEC likely reflects the efficacy of manifold improvements in broiler breeder production systems. A further reduction in AMR is still desirable.

Antimicrobial Susceptibility of Enterococcus Isolates from Cattle and Pigs in Portugal: Linezolid Resistance Genes optrA and poxtA

Enterococci are part of the commensal gut microbiota of mammals, with Enterococcus faecalis and Enterococcus faecium being the most clinically relevant species. This study assesses the prevalence and diversity of enterococcal species in cattle (n = 201) and pig (n = 249) cecal samples collected in 2017. Antimicrobial susceptibility profiles of E. faecium (n = 48) and E. faecalis (n = 84) were assessed by agar and microdilution methods. Resistance genes were screened through PCR and nine strains were analyzed by Whole Genome Sequencing. A wide range of enterococci species was found colonizing the intestines of pigs and cattle. Overall, the prevalence of resistance to critically important antibiotics was low (except for erythromycin), and no glycopeptide-resistant isolates were identified. Two daptomycin-resistant E. faecalis ST58 and ST93 were found. Linezolid-resistant strains of E. faecalis (n = 3) and E. faecium (n = 1) were detected. Moreover, oxazolidinone resistance determinants optrA (n = 8) and poxtA (n = 2) were found in E. faecalis (ST16, ST58, ST207, ST474, ST1178) and E. faecium (ST22, ST2138). Multiple variants of optrA were found in different genetic contexts, either in the chromosome or plasmids. We highlight the importance of animals as reservoirs of resistance genes to critically important antibiotics.

The Antibiotics Used in Livestock and Their Impact on Resistance in Enterococcus faecium and Enterococcus hirae on Farms in Gabon

The emergence of antibiotic resistance is a major concern around the world. The objective of this study was to investigate the antibiotics used in livestock and their impact on resistance in Enterococcus faecium and Enterococcus hirae on farms in Gabon. A structured questionnaire was used to collect information on the farms. Samples were collected from farms (n = 20) tested for Enterococcus by culture and isolation and were identified using a polymerase chain reaction (PCR) and sequencing. Antibiotic susceptibility was determined by the disc diffusion method on Mueller Hinton agar. The 20 farms included laying hens (6), swine (6), sheep (4) and cattle farms (4). Tetracycline was the most used antibiotic family (91%) and the most used prophylactic method (47%) for the treatment of animals. A total of 555 samples were collected and 515 (93%) Enterococcus spp. isolates of the genus were obtained. The prevalence of E. faecium and E. hirae were 10% and 8%, respectively. The isolates from E. faecium and E. hirae we found were related to clinical and human isolates in the NCBI database. E. faecium and E. hirae isolates showed a high resistance to tetracycline (69% and 65%) and rifampicin (39% and 56%). The tet(M) gene was detected in 65 tetracycline-resistant isolates with a large majority in hens (78% (21/27) and 86% (12/14) in E. faecium and E. hirae, respectively). The consumption of antibiotics favours the emergence of antibiotic resistance in animals in Gabon.

A review on non-thermal plasma treatment of water contaminated with antibiotics

Large amounts of antibiotics are produced and consumed worldwide, while wastewater treatment is still rather inefficient, leading to considerable water contamination. Concentrations of antibiotics in the environment are often sufficiently high to exert a selective pressure on bacteria of clinical importance that increases the prevalence of resistance. Since the drastic reduction in the use of antibiotics is not envisaged, efforts to reduce their input into the environment by improving treatment of contaminated wastewater is essential to limit uncontrollable spread of antibiotic resistance. This paper reviews recent progress on the use of non-thermal plasma for the degradation of antibiotics in water. The target compounds removal, the energy efficiency and the mineralization are analyzed as a function of discharge configuration and the most important experimental parameters. Various ways to improve the plasma process efficiency are addressed. Based on the identified reaction intermediates, degradation pathways are proposed for various classes of antibiotics and the degradation mechanisms of these chemicals under plasma conditions are discussed.

S. epidermidis Isolates from a Tertiary Care Portuguese Hospital Show Very High Antibiotic Non-Susceptible Rates and Significant Ability to Form Biofilms

Healthcare-associated infections (HAIs) have been increasing during recent decades, leading to long hospital stays and high morbidity and mortality rates. The usage of antibiotics therapy against these infections is enhancing the emergence of more multiple-drug resistant strains, in particular in Staphylococcus epidermidis. Hence, this study focused on the resistance pattern of S. epidermidis isolates from clinical settings and its association with phenotypic and molecular traits. Our results showed that HAIs were more prevalent among infants and older adults, and the most frequent type of HAI was central line-associated bloodstream infection. Half of the patients received antibiotic therapy before laboratory diagnosis. Preceding microbiological diagnosis, the number of patients receiving antibiotic therapy increased by 29.1%. Eighty-six per cent of the clinical isolates presented a multidrug resistance (MDR) profile, and a quarter were strong biofilm producers. Furthermore, polysaccharide intercellular adhesin (PIA)-dependent biofilms presented higher biomass production (p = 0.0041) and a higher rate of antibiotic non-susceptibility than PIA-independent biofilms, emphasizing the role of icaABDC operon in infection severity. Therefore, this study suggests that a thorough understanding of the phenotypic and molecular traits of the bacterial cause of the HAIs may lead to a more suitable selection of antibiotic therapy, improving guidance and outcome assessment.

Multidrug-Resistant Phenotypes of Escherichia coli Isolates in Wild Canarian Egyptian Vultures (Neophron percnopterus majorensis)

Simple Summary

Increasing antimicrobial resistance is a global problem for both human and animal health. Escherichia coli is frequently used as a “sentinel” for antimicrobial resistance and as an indicator of faecal contamination of the environment. This study is a characterisation of the antimicrobial resistance phenotypes of E. coli isolates obtained from cloacal samples of Canarian Egyptian vultures. A total of 65 chickens and 38 adult and immature birds were studied. Antimicrobial susceptibility to 16 antibiotics of 12 different categories was determined in 103 E. coli isolates. We found a 39.8% prevalence of multidrug-resistant (MDR) E. coli. Almost all MDR phenotypes found included resistance to tetracycline, an antibiotic widely used in veterinary medicine. Resistance has also been found to chloramphenicol (13 MDR phenotypes), imipenem (5 MDR phenotypes) and others. Wild birds can act as reservoirs and disseminators of MDR E. coli, transferring them via faeces to the environment, feed or water. Our results highlight the need to minimise exposure of wild birds to antimicrobials from human activities to avoid the spread of antimicrobial resistance.

Abstract

The presence of multidrug-resistant (MDR) Escherichia coli in cloacal samples from Canarian Egyptian vultures was investigated. Samples were obtained from chicks (n = 65) and from adults and immature birds (n = 38). Antimicrobial susceptibility to 16 antibiotics included in 12 different categories was determined for 103 E. coli isolates. MDR was defined as acquired non-susceptibility to at least one agent in three or more antimicrobial categories. Forty-seven different resistance phenotypes were detected: 31 MDR (41 isolates) and 16 non-MDR (62 isolates). One isolate was resistant to all 12 antimicrobial categories and 2 phenotypes included resistance to 9 antimicrobial categories. Imipenem resistance was included in five MDR phenotypes, corresponding to five different isolates. Statistically significant differences in prevalence of MDR-phenotypes were found between chicks in nests and the rest of the animals, probably due to the shorter exposure time of chicks to antimicrobials. The main risk derived from MDR bacteria in scavengers is that it threatens the treatment of wild animals in rescue centres and could be transferred to other animals in the facilities. In addition to this, it could pose a health risk to veterinarians or other staff involved in wildlife protection programmes.

Molecular diversity of Extended-spectrum β-lactamase-producing Escherichia coli from vultures in Canary Islands

Antimicrobial resistance among isolates from wild animals is increasingly reported. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, and particularly Escherichia coli, have spread worldwide as one of the most common multidrug-resistant organisms. The aim of this study was to determine the carriage rate of ESBL-producing E. coli isolates and their genetic characteristics in wild vultures from the Canary Islands. Faecal samples were collected from 22 apparently healthy free-ranging (wild) vulture chicks from Lanzarote and Fuerteventura (Canary Islands) during July 2019. They were seeded in MacConkey agar supplemented with cefotaxime (2 μg ml^-1 ). Colonies with typical morphology of E. coli were identified by MALDI-TOF-MS. Antimicrobial susceptibility was done by disk diffusion. Phenotypic detection of ESBL was performed by double-disk tests. The presence of bla_CTX-M , bla_SHV , bla_TEM , bla_KPC and bla_OXA-48 genes, as well as mcr-1 (colistin resistance), tetA/tetB and int1 gene, was tested by PCR/sequencing. Phylogenetic groups and multilocus sequence typing (MLST) were determined by PCR/sequencing. ESBL-producing E. coli isolates were detected in 5/22 tested animals (22.7%), and all isolates (one/animal) carried bla_CTX-M genes: bla_CTX-M-15 (n = 3) and bla_CTX-M-55 (n = 2). ESBL-positive isolates were ascribed to phylogenetic group D (two isolates), B₁ (two isolates) and A (one isolate), and five sequence types were detected (ST/phylogenetic-group/ESBL): ST515/B1/CTX-M-15, ST1290/A/CTX-M-15, ST38/D/CTX-M-15, ST457/D/CTX-M-55 and ST6448/B₁ /CTX-M-55; this suggests a genetic diversity among these isolates. Three CTX-M-15-producing isolates contained the bla_TEM gene and one the tetA gene. To our knowledge, this appears to be the first report of ESBL-producing E. coli in vulture chicks from the Canary Islands.

Occurrence and Antimicrobial Resistance Traits of Escherichia coli from Wild Birds and Rodents in Singapore

Antimicrobial resistance (AMR) in Escherichia coli (E. coli) poses a public health concern worldwide. Wild birds and rodents, due to their mobility, are potential vehicles for transmission of AMR bacteria to humans. Ninety-six wild birds’ faecal samples and 135 rodents’ droppings samples were collected and analysed in 2017. Forty-six E. coli isolates from wild birds and rodents were subjected to AMR phenotypic and genotypic characterisation. The proportion of E. coli isolates resistant to at least one of the antimicrobials tested from wild birds (80.8%) was significantly higher than that of isolates from rodents (40.0%). The proportion of E. coli isolates resistant to each antimicrobial class for wild birds was 3.8% to 73.1% and that for rodents was 5.0% to 35.0%. Six out of 26 E. coli isolates from wild birds (23.1%) and two out of 20 (10.0%) isolates from rodents were multi-drug resistant (MDR) strains. These MDR E. coli isolates were detected with various antimicrobial resistance genes such as bla_TEM-1B and qnrS1 and could be considered as part of the environmental resistome. Findings in this study suggested that wild birds and rodents could play a role in disseminating antimicrobial resistant E. coli, and this underscores the necessity of environment management and close monitoring on AMR bacteria in wild birds and rodents to prevent spreading of resistant organisms to other wildlife animals and humans.

Antimicrobial resistance genes present in the faecal microbiota of free-living Galapagos tortoises (Chelonoidis porteri)

Antimicrobial resistance (AMR), encoded by plasmid-mediated AMR genes (ARGs), is an increasing global public health threat. Wildlife play a fundamental role as sentinels, reservoirs and potential vectors of ARGs. For the first time in Galapagos, we have identified and quantified the presence of ARGs in free-living giant tortoises (Chelonoidis porteri). We performed ARG analyses by quantitative PCR of faeces collected from the cloaca of 30 tortoises widely distributed across Santa Cruz Island. Validated samples (n = 28) were analysed by a panel of up to 21 different ARGs and all 28 tortoise samples were positive to one or more genes encoding resistance. Thirteen of 21 tested ARGs were present in at least one sample, and 10 tortoises (35.7%) had a multi-resistant pattern. We recommend additional research so we may more fully understand resistance patterns across taxa and geographical locations throughout the Galapagos archipelago, and the implications of ARGs for the health of wildlife, domestic animals, and humans. In this study, we found 100% of sampled giant tortoises had ARGs present in their faeces, suggesting a large-scale distribution of these genes within the archipelago.

First report on extended-spectrum beta-lactamase (ESBL) producing Escherichia coli from European free-tailed bats (Tadarida teniotis) in Portugal: A one-health approach of a hidden contamination problem

The main aim of this study was to characterize the diversity of extended-spectrum beta-lactamases (ESBLs) in Escherichia coli isolates from European free tailed-bats (Tadarida teniotis) in Portugal. ESBL-producing E. coli isolates were recovered from 14 of 146 faecal samples (9.6%) and a total of 19 isolates were completely characterized. The more prevalent beta-lactamase genes detected were bla_CTX-M-1 (57.9%) and bla_CTX-M-3 (36.8%), followed by bla_SHV (31.6%), bla_TEM (21.1%), bla_OXA (10.5%) and bla_CTX-M-9 (10.5%). Among other associated resistance genes studied, tet(A) and tet(B) were predominant and fimA was the main virulence factor detected. Phylogroups D (47.4%) and A (31.6%) were the more prevalent, followed by group B2 (21.1%). Bats are reservoirs of antimicrobial-resistant bacteria and resistance determinants and is important in further studies to identify the main sources of pollution in the environment, such as water or insects that may contain these multiresistant organisms.

Planning a One Health Case Study to Evaluate Methicillin Resistant Staphylococcus aureus and Its Economic Burden in Portugal

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most important multidrug-resistant nosocomial pathogens worldwide with infections leading to high rates of morbidity and mortality, a significant burden to human and veterinary clinical practices. The ability of S. aureus colonies to form biofilms on biotic and abiotic surfaces contributes further to its high antimicrobial resistance (AMR) rates and persistence in both host and non-host environments, adding a major ecological dimension to the problem. While there is a lot of information on MRSA prevalence in humans, data about MRSA in animal populations is scarce, incomplete and dispersed. This project is an attempt to evaluate the current epidemiological status of MRSA in Portugal by making a single case study from a One Health perspective. We aim to determine the prevalence of MRSA in anthropogenic sources liable to contaminate different animal habitats. The results obtained will be compiled with existing data on antibiotic resistant staphylococci from Portugal in a user-friendly database, to generate a geographically detailed epidemiological output for surveillance of AMR in MRSA. To achieve this, we will first characterize AMR and genetic lineages of MRSA circulating in northern Portugal in hospital wastewaters, farms near hospitals, farm animals that contact with humans, and wild animals. This will indicate the extent of the AMR problem in the context of local and regional human-animal-environment interactions. MRSA strains will then be tested for their ability to form biofilms. The proteomes of the strains will be compared to better elucidate their AMR mechanisms. Proteomics data will be integrated with the genomic and transcriptomic data obtained. The vast amount of information expected from this omics approach will improve our understanding of AMR in MRSA biofilms, and help us identify new vaccine candidates and biomarkers for early diagnosis and innovative therapeutic strategies to tackle MRSA biofilm-associated infections and potentially other AMR superbugs.

Enhanced anti-microbial effect through cationization of a mono-triazatricyclodecane substituted asymmetric phthalocyanine

Antimicrobial photodynamic therapy (aPDT) is an effective way to combat infectious diseases and antibiotic resistance. Photosensitizer is a key factor of aPDT and has triggered extensive research interest. In this study, a new asymmetric Zn(II) phthalocyanine mono-substituted with a triazatricyclodecane moiety (compound 3) and its cationic N-methylated derivative (compound 4) were synthesized. Their photodynamic antimicrobial activities were evaluated using bioluminescent bacterial strains. Compound 3 showed phototoxicity only toward the Gram-positive bacteria, whereas the cationic derivative compound 4 exhibited strong anti-bacterial activity against both Gram-positive and Gram-negative strains. These bacterial species were eradicated (>4.0 logs or 99.99% killing) at appropriate concentrations of compound 4 with 12.7 J/cm² of red light, demonstrating compound 4 as a potent aPDT agent.

Poultry hatcheries as potential reservoirs for antimicrobial-resistant Escherichia coli: A risk to public health and food safety

Hatcheries have the power to spread antimicrobial resistant (AMR) pathogens through the poultry value chain because of their central position in the poultry production chain. Currently, no information is available about the presence of AMR Escherichia coli strains and the antibiotic resistance genes (ARGs) they harbor within hatchezries. Therefore, this study aimed to investigate the possible involvement of hatcheries in harboring hemolytic AMR E. coli. Serotyping of the 65 isolated hemolytic E. coli revealed 15 serotypes with the ability to produce moderate biofilms, and shared susceptibility to cephradine and fosfomycin and resistance to spectinomycin. The most common β-lactam resistance gene was bla_TEM, followed by bla_OXA-1, bla_MOX-like_,bla_CIT-like_,bla_SHV and bla_FOX. Hierarchical clustering of E. coli isolates based on their phenotypic and genotypic profiles revealed separation of the majority of isolates from hatchlings and the hatchery environments, suggesting that hatchling and environmental isolates may have different origins. The high frequency of β-lactam resistance genes in AMR E. coli from chick hatchlings indicates that hatcheries may be a reservoir of AMR E. coli and can be a major contributor to the increased environmental burden of ARGs posing an eminent threat to poultry and human health.

Rapid killing of bacteria by a new type of photosensitizer

Photodynamic antimicrobial chemotherapy (PACT) uses non-traditional mechanisms (free radicals) and is a highly advocated method with promise of inactivating drug-resistance bacteria for local infections. However, there is no related drug used in clinical practice yet. Therefore, new photosensitizers for PACT are under active development. Here, we report the synthesis of a series of photosensitizers with variable positive charges (ZnPc(TAP)₄ⁿ⁺, n = 0, 4, 8, 12) and their inactivation against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria. The binding kinetics of ZnPc(TAP)₄ⁿ⁺ to bacteria were measured by flow cytometer. Reactive oxygen species (ROS) generation mechanism of the photosensitizers was studied. The toxicity of these compounds to human blood cells was also evaluated. These compounds showed negligible toxicity against human erythocytes but potent bactericidal effects. The compound with 8 positive charges, ZnPc(TAP)₄⁸⁺, turned out to have the strongest antibacterial effect among this series of compounds, giving IC₅₀ value of 59 nM at a light dosage of 5 J/cm² toward E. coli. For a multi-resistant E. coli strain, ZnPc(TAP)₄⁸⁺ decreased the bacteria load by 1000-fold at a concentration of 1 μM. Interestingly, ZnPc(TAP)₄¹²⁺, instead of ZnPc(TAP)₄⁸⁺, exhibited the highest amount of binding to bacteria. Flow cytometry studies showed that all PSs have fast binding onto bacteria, reaching saturated binding within 5 min. Mechanistically, ZnPc(TAP)₄¹²⁺ generated ROS primarily via Type I mechanism, while ZnPc(TAP)₄⁴⁺ or ZnPc(TAP)₄⁸⁺ created ROS by both type I and type II mechanisms. ZnPc(TAP)₄ⁿ⁺ are highly potent, rapid-acting and non-toxic photosensitizers capable of inactivating bacteria.