Identification of shiga toxin and intimin coding genes in Escherichia coli isolates from pigeons (Columba livia) in relation to phylotypes and antibiotic resistance patterns

Characterization of Escherichia coli strains producing Shiga Toxin 2f subtype from domestic Pigeon

Shiga toxin-producing Escherichia coli (STEC) can cause mild diarrhea even severe hemolytic uremic syndrome (HUS). Shiga toxin (Stx) is the primary virulence factor. Two Stx types and several subtypes have been identified. STEC strains encoding stx2f (Stx2f-STECs) are frequently identified from pigeons. Stx2f was initially considered to be associated with mild symptoms, more recently Stx2f-STECs have been isolated from HUS cases, indicating their pathogenic potential. Here, we investigated the prevalence of Stx2f-STECs among domestic pigeons in two regions in China, characterized the strains using whole-genome sequencing (WGS), and assessed the Stx2f transcriptions. Thirty-two Stx2f-STECs (4.36%) were culture-positive out of 734 fecal samples (one strain per sample). No other stx subtype-containing strain was isolated. Four serotypes and two sequence types were determined, and a novel sequence type ST15057 was identified. All strains harbored the E. coli attaching and effacing gene eae. Two types of Stx2f prophages were assigned. Stx2f-STECs showed variable Stx transcription levels induced by mitomycin C. Whole genome single-nucleotide polymorphism (wgSNP) analysis revealed different genetic backgrounds between pigeon-derived strains and those from diarrheal or HUS patients. In contrast, pigeon-derived Stx2f-STECs from diverse regions exhibited genetic similarity. Our study reports the prevalence and characteristics of Stx2f-STECs from pigeons in China. The pigeon-derived strains might pose low public health risk.

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.

Detection of blaOXA-48 and mcr-1 Genes in Escherichia coli Isolates from Pigeon (Columba livia) in Algeria

The emergence and spread of β-lactams and colistin-resistant Escherichia coli in birds deserve a special concern worldwide. This study aimed to investigate the presence of β-lactams and colistin-resistant Escherichia coli strains isolated from the faeces of urban and rural pigeons in Batna, Algeria, and to characterise their molecular traits of resistance. Between March and April 2019, a total of 276 faecal droppings samples were collected in Batna, Algeria. Samples were subjected to selective isolation of β-lactams and colistin-resistant Escherichia coli. The representative colonies were then identified using Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry. Antimicrobial susceptibility testing was performed using the disc diffusion method. β-lactamases, as well as mcr genes, were screened for by PCR and confirmed by sequencing. Genetic relatedness of the mcr-positive E. coli strains was determined using multi-locus sequence typing analysis. Transferability features of carbapenemase genes were assessed by conjugation experiments. Overall, thirty-five E. coli isolates were obtained only from urban pigeon samples. All carbapenem-resistant isolates harboured the bla_OXA-48 gene as the only carbapenemase gene detected (n = 11), while bla_ESBL genes were detected in eighteen isolates. Out of the thirty-five isolates, four E. coli isolates were positive for the mcr-1 gene. The obtained mcr-1 positive E. coli isolates belonged to four STs, including ST1485, ST224, ST46, and a new ST. This study is the first to report the isolation of E. coli strains carrying the mcr-1 gene from pigeon faeces in Algeria and also the first to report the detection of bla_OXA-48-positive E. coli in pigeons. Close surveillance is, therefore, urgently needed to monitor the dissemination of bla_OXA-48 and mcr-1 producing E. coli strains in wildlife.

Pigeons as Carriers of Clinically Relevant Multidrug-Resistant Pathogens-A Clinical Case Report and Literature Review

Pigeons are widespread bird species in urban regions (Columba livia forma urbana) and may carry pathogens with zoonotic potential. In recent years, more and more data indicate that these zoonotic pathogens are multidrug resistant. Our results confirmed that global trend. Three different multidrug-resistant pathogens were isolated from an oral cavity of a racing pigeon with lesions typical for pigeon pox virus infection. Staphylococcus aureus was recognized as methicillin resistant, thus resistant to all beta-lactams. Additionally, it was also resistant to many other classes of antibiotics, namely: aminoglycosides, tetracyclines, phenicols, lincosamides, and macrolides. Escherichia coli showed resistance to all antimicrobials tested, and it was classified as intermediate to amikacin. Moreover, Candida albicans resistant to clotrimazole, natamycin, flucytosine, and amphotericin and intermediate to ketoconazole, nystatin, and econazole was also isolated. This raises the question how pigeons acquire such highly resistant strains. Therefore, more data are needed concerning the resistance to antibiotics in strains from domestic and wild pigeons in Poland. Until the problem is fully understood, it will be challenging to implement adequate planning of any control measures and check their effectiveness.

Domestic and game pigeons as reservoirs for Escherichia coli harbouring antimicrobial resistance genes

OBJECTIVES

In Iran, pigeons are kept and bred on the roofs of houses, which indicates the potential significance of pigeons in the dispersal of antimicrobial resistant Escherichia coli strains. Here we characterized antimicrobial resistance genotypes in relation to phenotypic presentations and phylogenetic backgrounds of the E. coli isolates from household pigeons in Kerman in southeast Iran.

METHODS

Totally, 152 faecal E. coli isolates from domestic and household pigeons were screened for 13 antimicrobial resistance genes, bla_TEM, bla_SHV, bla_CTX-M, sulI, sulII, dhfrI, dhfrV, aadA, aac(3)-I, tetA, tetB, floR and qnrA, by conventional polymerase chain reaction (PCR) technique. Clermont phylogenetic background of E. coli strains was studied and antibiotic resistance of all strains was assessed for seven antibiotics.

RESULTS

The antimicrobial resistance genes bla_TEM, tetA, tetB and aadA were detected in 52.6%, 6.5%, 6.5% and 5.9% of the isolates, respectively. PCR phylotyping revealed that a significant number of isolates within A₀ (54%), A₁ (70%), B1 (57.6%), B2₂ (75%) and D1 (87.5%) phylogroups were positive for the studied resistance genes. One phenotypic resistance pattern (trimethoprim-sulfamethoxazole) was associated with the presence of the corresponding gene sul2.

CONCLUSIONS

An alarming rate of phenotypic resistance was observed in this study. Many isolates were positive for the screened resistance genes. According to the phylogenetic background, most resistant isolates belonged to the commensal phylotypes, representing significant role of commensal strains as a source of resistance genes. These findings highlight the role of the pigeon as disseminator of resistant E. coli strains.

Are we overestimating risk of enteric pathogen spillover from wild birds to humans?

Enteric illnesses remain the second largest source of communicable diseases worldwide, and wild birds are suspected sources for human infection. This has led to efforts to reduce pathogen spillover through deterrence of wildlife and removal of wildlife habitat, particularly within farming systems, which can compromise conservation efforts and the ecosystem services wild birds provide. Further, Salmonella spp. are a significant cause of avian mortality, leading to additional conservation concerns. Despite numerous studies of enteric bacteria in wild birds and policies to discourage birds from food systems, we lack a comprehensive understanding of wild bird involvement in transmission of enteric bacteria to humans. Here, we propose a framework for understanding spillover of enteric pathogens from wild birds to humans, which includes pathogen acquisition, reservoir competence and bacterial shedding, contact with people and food, and pathogen survival in the environment. We place the literature into this framework to identify important knowledge gaps. Second, we conduct a meta‐analysis of prevalence data for three human enteric pathogens, Campylobacter spp., E. coli, and Salmonella spp., in 431 North American breeding bird species. Our literature review revealed that only 3% of studies addressed the complete system of pathogen transmission. In our meta‐analysis, we found a Campylobacter spp. prevalence of 27% across wild birds, while prevalence estimates of pathogenic E. coli (20%) and Salmonella spp. (6.4%) were lower. There was significant bias in which bird species have been tested, with most studies focusing on a small number of taxa that are common near people (e.g. European starlings Sturnus vulgaris and rock pigeons Columba livia) or commonly in contact with human waste (e.g. gulls). No pathogen prevalence data were available for 65% of North American breeding bird species, including many commonly in contact with humans (e.g. black‐billed magpie Pica hudsonia and great blue heron Ardea herodias), and our metadata suggest that some under‐studied species, taxonomic groups, and guilds may represent equivalent or greater risk to human infection than heavily studied species. We conclude that current data do not provide sufficient information to determine the likelihood of enteric pathogen spillover from wild birds to humans and thus preclude management solutions. The primary focus in the literature on pathogen prevalence likely overestimates the probability of enteric pathogen spillover from wild birds to humans because a pathogen must survive long enough at an infectious dose and be a strain that is able to colonize humans to cause infection. We propose that future research should focus on the large number of under‐studied species commonly in contact with people and food production and demonstrate shedding of bacterial strains pathogenic to humans into the environment where people may contact them. Finally, studies assessing the duration and intensity of bacterial shedding and survival of bacteria in the environment in bird faeces will help provide crucial missing information necessary to calculate spillover probability. Addressing these essential knowledge gaps will support policy to reduce enteric pathogen spillover to humans and enhance bird conservation efforts that are currently undermined by unsupported fears of pathogen spillover from wild birds.

Molecular characterization, genetic diversity and antibacterial susceptibility of Escherichia coli encoding Shiga toxin 2f in domestic pigeons

This study aimed to evaluate prevalence, characteristics, genotypic diversity and antibacterial susceptibility of Escherichia coli encoding Shiga toxin 2f in domestic pigeons in different provinces of Iran. A total of 117 faecal samples were collected from pigeons and were subjected to molecular detection of stx2f. In total, 20, 25·8, 21·4 and 9% of pigeons from Tehran, Ferdows, Garmsar and Babol cities carried stx2f+ isolates, respectively. Of the 460 E. coli isolates examined, 43 were stx2f+ and most also carried eae (95·3%) and astA (97·7%) genes. Some of the stx2f+ isolates harboured cnf (9·3%), but all were negative for stx1, stx2 (other subtypes) and ehly. Most Strains (90%) were assigned to B1 phylogroup and possessed Intimin-β. Fingerprinting of the stx2f+ isolates using either enterobacterial repetitive intergenic consensus sequences (ERIC) or random amplified polymorphic DNA (RAPD)-polymerase chain reaction revealed seven distinct profiles by each method, with one prevailing (65·1 and 46·5%, respectively). By the combination of methods, 10 profiles were recognized. Ten isolates from different profiles were shown to belong to O20, O78 and O115 serogroups, and eight were 100% identical in the stx2f gene sequence. The strains were consistently resistant to amoxicillin and lincospectin and commonly resistant to tetracycline (88·4%) and doxycycline (74·4%). Overall, the results indicate a limited degree of genetic diversity in stx2f-harbouring E. coli from pigeons. Significance and impact of the study: Carriage of stx2f gene tends to be underreported in pigeon Escherichia coli isolates because most routine genetic and phenotypic tests cannot efficiently target this gene or detect the toxin. Nevertheless, pigeons frequently carry E. coli strains that are stx2f-positive, and this situation is not limited to any distinct geographical area. The current results suggest that genetic background of stx2f-encoding E. coli is distinct from most Shiga toxin-producing E. coli strains. However, the factors that contribute to host preferences and pathogenicity remain unclear. These findings have public health significance that should be addressed in future research.