World Health Organization critical priority Escherichia coli clone ST648 in magnificent frigatebird (Fregata magnificens) of an uninhabited insular environment

Steady existence of Escherichia coli co-resistant to carbapenem and colistin in an animal breeding area even after the colistin forbidden

Carbapenem- and colistin-resistant Escherichia coli (CCREC) cause high mortality rates and health costs, and have become serious health concerns. Total 1764 samples were collected from 60 animal farms in 2019 and 2021, including worker and animal faeces, wastewater, well water, air, vegetables, human hands, object surfaces, throat swabs, soil, and flies to investigate the prevalence and potential transmission pathways of CCREC. Eleven CCREC were detected: 9 (5 in 2019 and 4 in 2021) from 5 worker faeces, 3 animal faeces, 1 wastewater, and 2 from 1 flies sample. Chicken farms had the highest number of CCREC (n = 9). The detection rate was low (<1.1%) overall, and there was no significant difference in both years, indicating that CCREC existed stably after 4 years of colistin ban. The combinations of chromosomes and plasmids harbouring blaNDM and mcr-1.1 were divided into 4 patterns: IncX3 plasmid-blaNDM & chromosome-mcr.1.1 (n = 5); IncX3 plasmid-blaNDM & IncHI2 plasmid-mcr.1.1 (n = 3); IncFII plasmid-blaNDM & IncI2 plasmid-mcr.1.1 (n = 2); both chromosome (n = 1). The blaNDM located on plasmids was surrounded by similar genetic structures: Tn3-IS-blaNDM-bleMBL-TrpF-DsbD-IS. The genetic contexts of mcr-1.1 were highly similar, with 'ISApl1-mcr-1.1-PAP2' and 'mcr-1.1-PAP2'. All plasmids can be successfully transferred into E. coli J53, except for the IncHI2 plasmids with the transfer rate of 33.3%. The IncFII and IncI2 plasmids from same strain of flies could be co-transferred. The clonal spread of CCREC from humans to humans occurred on the same pig farm (P4) or different chicken farms (BC9 and LH7). This study suggested that flies, chromosomes, and plasmids jointly contribute to the steady existence of CCREC.

ESBL-producing Escherichia coli prevalence and sharing across seabirds of central Chile

Antimicrobial resistance (AMR) is a major global public threat, now largely reported in natural environments. Seabirds are carriers of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli), but different foraging and breeding behaviour could impact ESBL-E. coli circulation. We compared the prevalence and genetic determinants of ESBL-E. coli from resident Kelp gulls (Larus dominicanus, Ld), migratory Franklin's gulls (Larus pipixcan, Lp), and endemic Peruvian pelicans (Pelecanus thagus, Pt) from the Humboldt Current Ecosystem (HCE) of central Chile. From 2020 to 2022, we collected 699 fresh faecal samples (Ld = 449, Lp = 116, Pt = 134), and isolated 271 ESBL-E. coli (39 %). Whole-genome-sequencing (WGS) was performed on 85 E. coli selected isolates to identify their Sequence Type (ST), AMR genes, virulence genes, mobile genetic elements (MGE), and to assess potential interspecies transmission. ESBL-genes were detected in the remaining ESBL-E. coli isolates by PCR. ESBL-E. coli prevalence in Ld (46 % [CI: 42-51 %]) and Pt (34 % [CI: 27-43 %]) was higher than in Lp (15 % [CI: 9-22 %]). WGS revealed 41 ESBL-E. coli STs including pandemic clones ST10, ST58, ST131 and ST410. The blaCTX-M-1 and blaCTX-M-15 genes were the most prevalent among ESBL genes, and were mostly associated with MGE IncI1-I(Alpha) and ISEc9. We also report the pAmpC blaCMY-2 gene associated to MGE Inc1-I(Alpha) and IS640 in two E. coli from a Ld and a Lp. Eight ESBL-E. coli of the same ST were shared by at least two seabird species, including ST10 (Ld and Pt); ST88, ST410 and ST617 (Pt and Lp); ST38, ST58, ST131, and SST1722 (three species). Single nucleotide polymorphism (SNP) phylogenetic analyses of ST38, ST617 and ST1722 showed a low difference of SNPs between STs found in different seabird species, suggesting ESBL-E. coli clonal exchanges. Our results highlight ESBL-E. coli dissemination across seabirds of the HCE, including species that unusually forage on human waste like pelicans.

Antibiotic-resistant characteristics and horizontal gene transfer ability analysis of extended-spectrum β-lactamase-producing Escherichia coli isolated from giant pandas

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) is regarded as one of the most important priority pathogens within the One Health interface. However, few studies have investigated the occurrence of ESBL-EC in giant pandas, along with their antibiotic-resistant characteristics and horizontal gene transfer abilities. In this study, we successfully identified 12 ESBL-EC strains (8.33%, 12/144) out of 144 E. coli strains which isolated from giant pandas. We further detected antibiotic resistance genes (ARGs), virulence-associated genes (VAGs) and mobile genetic elements (MGEs) among the 12 ESBL-EC strains, and the results showed that 13 ARGs and 11 VAGs were detected, of which bla CTX-M (100.00%, 12/12, with 5 variants observed) and papA (83.33%, 10/12) were the most prevalent, respectively. And ISEcp1 (66.67%, 8/12) and IS26 (66.67%, 8/12) were the predominant MGEs. Furthermore, horizontal gene transfer ability analysis of the 12 ESBL-EC showed that all bla CTX-M genes could be transferred by conjugative plasmids, indicating high horizontal gene transfer ability. In addition, ARGs of rmtB and sul2, VAGs of papA, fimC and ompT, MGEs of ISEcp1 and IS26 were all found to be co-transferred with bla CTX-M. Phylogenetic analysis clustered these ESBL-EC strains into group B2 (75.00%, 9/12), D (16.67%, 2/12), and B1 (8.33%, 1/12), and 10 sequence types (STs) were identified among 12 ESBL-EC (including ST48, ST127, ST206, ST354, ST648, ST1706, and four new STs). Our present study showed that ESBL-EC strains from captive giant pandas are reservoirs of ARGs, VAGs and MGEs that can co-transfer with bla CTX-M via plasmids. Transmissible ESBL-EC strains with high diversity of resistance and virulence elements are a potential threat to humans, animals and surrounding environment.

Gram-negative bacterial diversity and evidence of international clones of multidrug-resistant strains in zoo animals

Enterobacterales and Pseudomonas aeruginosa have been colonizing or infecting wild hosts and antimicrobial-resistant strains are present in mammals and birds. Furthermore, international high-risk clones of multidrug-resistant Escherichia coli are identified and the implications of multidrug-resistant Gram-negative bacteria in zoo animals are discussed.

ESBL-Producing Enterobacterales at the Human-Domestic Animal-Wildlife Interface: A One Health Approach to Antimicrobial Resistance in Piauí, Northeastern Brazil

The use, misuse, and overuse of antimicrobials is one of the main public health threats of the 21st century. We investigated the risk factor of the presence of extended-spectrum, cephalosporin-resistant Enterobacterales in feces of non-domestic and domestic birds and other domestic animals in Piauí State, northeast Brazil. We collected a total of 387 cloacal and rectal swab samples of free-living birds, domestic birds, and domestic mammals in five municipalities: Amarante, Água Branca, Lagoa Alegre, Parnaíba, and Teresina. A total of 59/387 (15.2%) of these samples harbored extended spectrum beta-lactamase (ESBL)-producing Enterobacterales. Using the MALDI-TOF technique, we identified fifty-seven samples as Escherichia coli and two samples as Klebsiella pneumoniae. Teresina and Parnaíba had the highest prevalence of animals with resistant bacteria (32.1% and 27.1%, respectively) and highest exposure risk factor (OR of 16.06 and 8.58, respectively, and p < 0.001 for all). Multidrug-resistant, ESBL-producing Enterobacterales were observed in 72.8% of the samples (43/59). For the free-living birds, the positive samples belonged to a great kiskadee (Pitangus sulphuratus) and a semipalmated sandpiper (Calidris pusilla) in migratory and resident species, respectively. For domestic animals, the swine samples showed the highest prevalence of antimicrobial resistance. The lack of access to veterinary care and information regarding antimicrobial therapy, along with the easy access to antimicrobials without medical prescription, favors the inadequate use of antimicrobials in Piauí.

Molecular Characterization of Escherichia coli Causing Urinary Tract Infections Through Next-Generation Sequencing: A Comprehensive Analysis of Serotypes, Sequence Types, and Antimicrobial and Virulence Genes

Introduction An enormous increase in antimicrobial resistance (AMR) among bacteria isolated from human clinical specimens contributed to treatment failures. Increased surveillance through next-generation sequencing (NGS) or whole genome sequencing (WGS) could facilitate the study of the epidemiology of drug-resistant bacterial strains, resistance genes, and other virulence determinants they are potentially carrying. Methods This study included 30 Escherichia coli (E. coli) isolates obtained from patients suffering from urinary tract infections (UTIs) attending Prathima Institute of Medical Sciences, Karimnagar, India. All bacterial isolates were identified, and antimicrobial susceptibility patterns were determined through conventional microbiological techniques and confirmed by automated systems. All the isolates were investigated using NGS to identify genes coding for resistance, such as extended-spectrum beta-lactamases (ESBLs), metallo-beta-lactamases, and virulence genes. Multilocus sequence typing (MLST) was used to understand the prevalent strain types, and serotyping was carried out to evaluate the type of O (cell wall antigen) and H (flagellar antigen) serotypes carried by the isolates. Results The conventional antimicrobial susceptibility testing revealed that 15 (50%) isolates were resistant to imipenem (IPM), 10 (33.33%) were resistant to amikacin (AK), 13 (43.33%) were resistant to piperacillin-tazobactam (PTZ), 17 (56.66%) were resistant to cephalosporins, and 14 (46.66%) were resistant to nitrofurantoin (NIT). Among the isolates, 26 (86.66%) had revealed the presence of multiple antibiotic-resistant genes with evidence of at least one gene coding for beta-lactamase resistance. There was a high prevalence of blaCTX-M (19/30, 63.33%) genes, followed by blaTEM and blaOXA-1. The blaNDM-5 gene was found in three isolates (3/30, 10%). The virulence genes identified in the present study were iutA, sat, iss, and papC, among others. The E. coli serotype found predominantly belonged to O25:H4 (5, 16.66%), followed by O102:H6 (4, 13.33%). A total of 16 MLST variants were identified among the examined samples. Of the MLST-based sequence types (STs) identified, ST-131 (7, 23.33%) was the predominant one, followed by ST-167 (3, 10%) and ST-12 (3, 10%). Conclusions The study results demonstrated that the E. coli strains isolated from patients suffering from UTIs potentially carried antimicrobial resistance and virulence genes and belonged to different strain types based on MLST. Careful evaluation of bacterial strains using molecular analyses such as NGS could facilitate an improved understanding of bacterial antibiotic resistance and its virulence potential. This could enable physicians to choose appropriate antimicrobial agents and contribute to better patient management, thereby preventing the emergence and spread of drug-resistant bacteria.

Survey of selected viral agents (herpesvirus, adenovirus and hepatitis E virus) in liver and lung samples of cetaceans, Brazil

Hepatic and pulmonary lesions are common in cetaceans, despite their poorly understood viral etiology. Herpesviruses (HV), adenoviruses (AdV) and hepatitis E virus (HEV) are emerging agents in cetaceans, associated with liver and/or pulmonary damage in mammals. We isolated and molecularly tested DNA for HV and AdV (n = 218 individuals; 187 liver and 108 lung samples) and RNA for HEV (n = 147 animals; 147 liver samples) from six cetacean families. All animals stranded or were bycaught in Brazil between 2001 and 2021. Positive-animals were analyzed by histopathology. Statistical analyses assessed if the prevalence of viral infection could be associated with the variables: species, family, habitat, region, sex, and age group. All samples were negative for AdV and HEV. Overall, 8.7% (19/218) of the cetaceans were HV-positive (4.8% [9/187] liver and 11.1% [12/108] lung), without HV-associated lesions. HV-prevalence was statistically significant higher in Pontoporiidae (19.2%, 10/52) when compared to Delphinidae (4.1%, 5/121), and in southeastern (17.1%, 13/76)-the most industrialized Brazilian region-when compared to the northeastern region (2.4%, 3/126). This study broadens the herpesvirus host range in cetaceans, including its description in pygmy sperm whales (Kogia breviceps) and humpback whales (Megaptera novaeangliae). Further studies must elucidate herpesvirus drivers in cetaceans.

Snapshot of resistome, virulome and mobilome in aquaculture

Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of Gram-negative bacteria isolated in seabream and bivalve molluscs, using a WGS approach. Sixty-six Gram-negative strains (Aeromonadaceae, Enterobacteriaceae, Hafniaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Vibrionaceae, and Yersiniaceae families) were selected for genomic characterization. The species and MLST were determined, and antibiotic/disinfectants/heavy metals resistance genes, virulence determinants, MGE, and pathogenicity to humans were investigated. Our study revealed new sequence-types (e.g. Aeromonas spp. ST879, ST880, ST881, ST882, ST883, ST887, ST888; Shewanella spp. ST40, ST57, ST58, ST60, ST61, ST62; Vibrio spp. ST206, ST205). >140 different genes were identified in the resistome of seabream and bivalve molluscs, encompassing genes associated with β-lactams, tetracyclines, aminoglycosides, quinolones, sulfonamides, trimethoprim, phenicols, macrolides and fosfomycin resistance. Disinfectant resistance genes qacE-type, sitABCD-type and formA-type were found. Heavy metals resistance genes mdt, acr and sil stood out as the most frequent. Most resistance genes were associated with antibiotics/disinfectants/heavy metals commonly used in aquaculture settings. We also identified 25 different genes related with increased virulence, namely associated with adherence, colonization, toxins production, red blood cell lysis, iron metabolism, escape from the immune system of the host. Furthermore, 74.2 % of the strains analysed were considered pathogenic to humans. We investigated the genetic environment of several antibiotic resistance genes, including blaTEM-1B, blaFOX-18, aph(3″)-Ib, dfrA-type, aadA1, catA1-type, tet(A)/(E), qnrB19 and sul1/2. Our analysis also focused on identifying MGE in proximity to these genes (e.g. IntI1, plasmids and TnAs), which could potentially facilitate the spread of resistance among bacteria across different environments. This study provides a comprehensive examination of the diversity of resistance genes that can be transferred to both humans and the environment, with the recognition that aquaculture and the broader environment play crucial roles as intermediaries within this complex transmission network.

Molecular characterization of highly prevalent Escherichia coli and Escherichia marmotae resistant to extended-spectrum cephalosporins in European starlings (Sturnus vulgaris) in Tunisia

European starlings are widespread migratory birds that have already been described as carrying bacteria resistant to extended-spectrum cephalosporins (ESC-R). These birds are well known in Tunisia because they spend the wintertime in this country and are hunted for human consumption. The goal of our study was to estimate the proportion of ESC-R in these birds and to characterize the collected isolates using whole-genome sequencing. Results showed that 21.5% (42/200) of the birds carried either an extended-spectrum beta-lactamase (ESBL) or an acquired AmpC gene. Diverse bla CTX-M genes were responsible for the ESBL phenotype, bla CTX-M-14 being the most prevalent, while only bla CMY-2 and one bla CMY-62 were found in AmpC-positive isolates. Likewise, different genetic determinants carried these resistance genes, including IncHI2, and IncF plasmids for bla CTX-M genes and IncI1 plasmids for bla CMY-2 genes. Three chromosomally encoded bla CTX-M-15 genes were also identified. Surprisingly, species identification revealed a large proportion (32.7%) of Escherichia marmotae isolates. This species is phenotypically indistinguishable from Escherichia coli and has obviously the same capacity to acquire ESC-R genes. Our data also strongly suggest that at least the IncHI2/pST3 plasmid can spread equally between E. coli and E. marmotae. Given the potential transmission routes between humans and animals, either by direct contact with dejections or through meat preparation, it is important to closely monitor antimicrobial resistance in European starlings in Tunisia and to set up further studies to identify the sources of contamination of these birds. IMPORTANCE The One Health concept highlighted knowledge gaps in the understanding of the transmission routes of resistant bacteria. A major interest was shown in wild migratory birds since they might spread resistant bacteria over long distances. Our study brings further evidence that wild birds, even though they are not directly submitted to antibiotic treatments, can be heavily contaminated by resistant bacteria. Our results identified numerous combinations of resistance genes, genetic supports, and bacterial clones that can spread vertically or horizontally and maintain a high level of resistance in the bird population. Some of these determinants are widespread in humans or animals (IncHI2/pST3 plasmids and pandemic clones), while some others are less frequent (atypical IncI1 plasmid and minor clones). Consequently, it is essential to be aware of the risks of transmission and to take all necessary measures to prevent the proportions of resistant isolates from increasing uncontrollably.

Detection of Escherichia coli and other Enterobacteriales members in seabirds sampled along the Brazilian coast

Escherichia coli, an Enterobacterales member, is a normal representative of the microbiota of homeothermic animals. Most strains are commensal, but several pathotypes can cause disease, and numerous antimicrobial resistance factors have been identified. These bacteria have spread rapidly in recent years, highlighting the importance of screening the environment and non-human reservoirs for virulent strains and/or those presenting resistance factors, in addition to other microorganisms of public health importance. In this context, this study aimed to survey Enterobacteriales present in seabirds sampled along the Brazilian coast, comparing findings between migratory and resident birds, as well as between wrecked and non-wrecked animals. Escherichia coli pathotypes were also characterized through rapid seroagglutination and polymerase chain reaction techniques and antimicrobial resistance profiles were investigated through the disc agar diffusion method. Cloacal, ocular, oral, tracheal, and skin lesion swabs, as well as fresh feces, were collected from 122 seabirds. The findings indicate these animals as important hosts for opportunistic human pathogens. Escherichia coli strains were identified in 70 % of the analyzed seabirds, 62 % of which displaying resistant or intermediate profiles to at least one antimicrobial, while 7% were multiresistant. Resistance to tetracycline (22 %), nalidixic acid (15 %), trimethoprim-sulfamethozaxol (14 %) and ampicillin (12 %) were the most prevalent. Resistance to cefoxitin, a critically important antimicrobial for human medicine, was also detected. Virulence genes for one of the EAEC, ETEC or EPEC pathotypes were detected in 30 % of the identified strains, the first two described in seabirds for the first time. The EAEC gene was detected in 25 % of the sampled seabirds, all resident, 8 % of which exhibited a multidrug-resistant profile. Thus, seabirds comprise important reservoirs for this pathotype. Escherichia coli was proven an ubiquitous and well-distributed bacterium, present in all evaluated bird species and sampling sites (except Marajó Island). According to the chi-square test, no significant differences between E. coli prevalences or antimicrobial resistance profiles between migratory and resident and between wrecked and non-wrecked seabirds were observed. Thus, migratory birds do not seem to contribute significantly to E. coli frequencies, pathotypes or antimicrobial resistance rates on the Brazilian coast.

Antibiotic resistant Escherichia coli in wild birds hospitalised in a wildlife rescue centre

The aim of this work was to evaluate the consequence of a hospitalisation period on antimicrobial resistance in Escherichia coli isolated from wild bird species admitted in the wildlife rescue centre of the Department of Veterinary Sciences (Turin University, Italy). Samples were collected from 121 raptors and 51 synanthropic animals, at the time of arrival as well as 5 and 10 days afterwards for a total of 372 faecal samples, and the susceptibility of E. coli strains was tested to a panel of seven antibacterials. Of the total, 109 animals (63.37 %) presented at least one sample positive for E. coli, 36 strains (39.6 %) were multi-drug resistant (MDR) and 12 (13.2 %) were extended spectrum beta-lactamase (ESBL)-producing E. coli. During the first 10 days of hospitalisation E. coli strains increased the number of resistances towards each antimicrobial principle, the number of ESBL E. coli and the therapy with fluoroquinolones developed resistance towards ceftriaxone, marbofloxacin, sulfamethoxazole-trimethoprim and tetracycline. Our results suggest that wild birds act as reservoirs of MDR bacteria, being potential sources for their spreading in the environment and to other species.