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

Competitive relationships due to similar nutrient preferences reshape soil bacterial metacommunities

Paddy soil, as an ecosystem with alternating drained and flooded conditions, microorganisms in it can maintain the stability of the ecosystem by regulating the composition and diversity of its species when disturbed by external biotic or abiotic factors, and the regulatory mechanism in this process is a controversial topic in ecological research. In this study, we investigate the effects of pigeon feces addition on bacterial communities in three textured soils, two conditions (drained and flooded) based on microcosm experiment using high-throughput sequencing techniques. Our results show that pigeon feces addition reduced environmental heterogeneity and community diversity, both under flooded and drained conditions and in all textured soils, thereby decreasing the effectiveness of environmental selection and increasing diffusion limitations among bacterial communities. Bacterial communities are altered by environmental factors including total organic carbon, available nitrogen, total phosphorus, available phosphorus and available potassium, resulting in the formation of new community structures and dominant genera. Bacteria from pigeon feces did not colonize the original soil in large numbers, and the soil bacterial community structure changed, with some species replaced the indigenous ones as new dominant genera. As nutrient diffusion increases the nutrient content of the soil, this does not lead to species extinction; however, nutrient diffusion creates new nutrient preferences of the bacterial community, which causes direct competition between species, and contributes to the extinction and immigration species. Our results suggest that species replacement is an adaptive strategy of soil bacterial community in response to dispersal of pigeon feces, and that bacterial community regulate diversity and abundance of the community by enhancing species extinction and immigration, thereby preventing bacteria in pigeon feces from colonizing paddy soils and maintaining ecosystem stability.

Molecular detection of multidrug and methicillin resistance in Staphylococcus aureus isolated from wild pigeons (Columba livia) in South Africa

Staphylococcus aureus is an important human and veterinary pathogen. The present study aimed to determine the prevalence of antibiotic resistance among S. aureus isolated from samples obtained from free-flying wild pigeons and houseflies from different locations surrounding a local hospital in the Greater Durban area in KwaZulu-Natal Province, South Africa. Environmental fecal samples were obtained from wild pigeons that inhabits the grounds of a local public hospital located on the South Beach area, Durban, South Africa. Housefly samples were collected from three different locations (Kenneth Stainbank Nature Reserve, Montclair/Clairwood, and Glenwood/Berea) in the greater Durban area, all within a close proximity to the hospital. Following enrichment, identification, and antimicrobial resistance profiling, S. aureus isolates were subjected to DNA extraction using the boiling method. It was found that 57 out of 252 samples (22.62%) were positive for S. aureus. The Kirby-Bauer disk diffusion method of antibiotic susceptibility testing was performed and revealed that antibiotic resistance rates to penicillin and rifampicin were the most common, with both returning 48 (84.2%) out of the 57 S. aureus isolates being resistant to penicillin and rifampicin. Antibiotic resistance rates to clindamycin, linezolid, erythromycin, tetracycline, cefoxitin, and ciprofloxacin were 82.5%, 78.9%, 73.7%, 63.2%, 33.3%, and 15.8% respectively. Antibiotic resistance genes were detected using primer-specific PCR and it was found that the prevalence rates of tetM, aac(6')-aph(2″), mecA, tetK, ermc, and blaZ genes were 66.7%, 40.4%, 40.4%, 38.6%, 24.6%, and 3.51% respectively. Statistical analysis revealed significant (p < 0.05) relationships between the tetM, aac(6')-aph(2″), and ermC genes and all parameters tested. A significant correlation between the aac(6')-aph(2″) gene and the tetM (0.506) and ermC (-0.386) genes was identified. It was found that 23 (40.3%) S. aureus isolates were mecA positive, of which 10 (52.6%) out of 19 cefoxitin-resistant isolates were mecA positive and 13 (35.1%) out of 37 cefoxitin-sensitive isolates were mecA positive. The results of the present study demonstrated the detection of methicillin and multidrug resistant S. aureus isolated from samples obtained from wild pigeons and houseflies in the surroundings of a local public hospital in the Greater Durban area in South Africa. The findings of the study may account for the emergence of multidrug-resistant staphylococcal infections. The findings highlight the significant role of wild pigeons and houseflies in the spread of drug-resistant pathogenic S. aureus including MRSA. The conclusions of the present study highlight the improtant role of wildlife and the environment as interconnected contributors of One Health.

DISTRIBUTION AND ANTIMICROBIAL RESISTANCE OF STAPHYLOCOCCI ISOLATED FROM FREE-LIVING SOUTH AMERICAN COATI (NASUA NASUA) IN AN URBAN PARK IN MINAS GERAIS, BRAZIL

The scientific information regarding staphylococci in procyonids is scarce. Hence, the aim of this study was to evaluate the frequency, distribution, and pattern of antimicrobial resistance of staphylococcal species isolated from free-roaming coatis (Nasua nasua) in an urban park in Belo Horizonte, Minas Gerais, Brazil. Rectal swabs from 55 free-living coatis were plated onto mannitol salt agar for isolating staphylococci, and species were identified using matrix-assisted laser desorption/ionization-time of flight mass spectrometry, polymerase chain reaction (PCR) of nuc, and sequencing of 16S rRNA and rpoB when needed. Antimicrobial susceptibility was investigated using the disk diffusion method, and the presence of the mecA gene was investigated by PCR. A total of 72.7% of the animals tested positive for staphylococci. Nine different species were identified, and Staphylococcus intermedius (60.4%) and S. delphini (20.9%) were the most frequently isolated species. Most of the isolates were susceptible to most of the antimicrobials evaluated, with a resistance pattern seen for penicillin (13.9%). One isolate was multidrug-resistant (MDR). The present study suggests that coatis are natural hosts of S. intermedius and S. delphini and, despite living in a heavily anthropized environment, the Staphylococcus spp. isolates showed a low incidence of drug resistance.

Pathological and molecular identification of Mycobacterium avium infection in a loft of domestic pigeons (Columba livia var. domestica) from India

Mycobacterium avium is a zoonotic pathogen associated with a wide range of pulmonary and extrapulmonary manifestations in a range of host species like humans, animals, and birds. The disease is more common in the avian population, and opportunistic infections have been reported in immune-compromised or debilitated animals and humans. This study reports the pathological and molecular identification of Mycobacterium avium causing avian mycobacteriosis in a loft of domestic pigeons (Columba livia var. domestica). Out of 30 pigeons aged 2-3 years, ten adult racing pigeons revealed a severe chronic and debilitating disease followed by death. The clinical signs included chronic emaciation, dullness, ruffled feathers, lameness, and greenish, watery diarrhea. Post-mortem examination of birds revealed multifocal gray- to yellow-colored raised nodules in the liver parenchyma, spleen, lungs, intestines, bone marrow, and joints. Avian mycobacteriosis was suspected based on the tissue impression smears stained by Ziehl-Neelsen staining. Histopathological examination also revealed multifocal granulomatous lesions in affected organs, which is characteristic of avian mycobacteriosis. The PCR analysis based on 16S rRNA, IS1245, and IS901 regions suggested the presence of Mycobacterium avium infection belonging to either subspecies avium or sylvaticum. This is the first detailed report of avian mycobacteriosis in pigeons from India, warranting a strict surveillance program to identify the carrier status of these microorganisms in the pigeons, which may prove a fatal zoonotic infection in humans.

Distribution of virulence-associated genes, antibiotic resistance and phylogenetic groups in Escherichia coli isolated from domestic and racing pigeons

Despite a lot of information about virulence and resistance of Escherichia coli (E. coli) in poultry, very limited data are currently available on its occurrence in pigeon isolates, although this poses a threat to human and animal health. Therefore, this study was conducted to explore the phylogenetic classification, antibiotic sensitivity, and virulence factors in E. coli isolated from cloacal swabs of domestic pigeons bred for meat (n = 47) and racing pigeons (n = 44). The most frequent phylogroup in racing pigeons was E (36, 82.00%), unlike domestic pigeons (B2- 19, 40.00%). The most abundant iron uptake system in both groups of bird was feoB (racing = 40, 90.90%; domestic = 44, 93.61%). The presence of ibeA (52, 57.10%) and kpsMTII (46, 50.50%) genes was detected in more than half of all strains belonging exclusively to phylogroups B2, D, E, F, clade I. Antibiotic resistance was higher in racing pigeons. All racing pigeon isolates were resistant to tetracycline and trimethoprim + sulphonamide. Resistance to ciprofloxacin was determined in three isolates (6.38%) of domestic and 33 isolates (75%) of racing pigeons. Aminoglycosides and β-lactamases resistance were also recorded. One of the important detected phenotypic mechanisms of resistance occurring in isolates from racing pigeons was AGL AAC(6´)I. Our study confirms that healthy pigeons are a reservoir of antibiotic-resistant E. coli containing an arsenal of virulence factors, thus capable of potentially causing infection. Pigeons with the option to fly to multiple places can transfer virulent and resistant bacteria. Direct contact with pigeons and their faeces and the contamination of water and food pose a threat of infection to humans and other animal species.

Staphylococcal species composition in the skin microbiota of domestic pigeons (Columba livia domestica)

Staphylococci are a natural component of the skin microbiota of many organisms, including humans and birds. As opportunistic pathogens, they can cause a variety of infections in humans. The close contact between domestic pigeons and their owners provide an opportunity for exchange of skin-associated bacteria. In this study, 41 healthy racing pigeons were tested. Staphylococci were detected on the skin of each bird (41/41, 100%). Isolates were identified at the species level using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). The diversity of the Staphylococcus species was relatively high and coagulase-negative staphylococci (CoNS) were predominantly isolated. In total, ten different staphylococcal species were identified. S. lentus (19/41, 46.3%) was noted most frequently. The pigeon skin was also inhabited by S. xylosus (6/41, 14.6%), S. equorum (4/41, 9.8%), S. hyicus (3/41, 7.3%), S. intermedius (2/41, 4.9%), S. sciuri (2/41, 4.9%), S. vitulinus (2/41, 4.9%), S. lugdunensis (1/41, 2.4%), S. hominis (1/41, 2.4%), and S. auricularis (1/41, 2.4%). Our results indicate that domestic pigeons may carry pathogens with zoonotic potential. All strains were susceptible to 12 antibiotics (ciprofloxacin, clindamycin chloramphenicol, erythromycin, fosfomycin, gentamicin, levofloxacin, norfloxacin, rifampicin, tobramycin, trimethoprim/sulfamethoxazole, vancomycin) representing 8 different classes. None isolate displayed a multidrug-resistant phenotype. Resistance to tetracycline (6/41, 14.6%) and to penicillin (4/41, 9.7%) was shown. The mecA gene was not detected in the examined strains and no methicillin-resistant staphylococci were found on the skin of the healthy pigeons.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Staphylococcus aureus in cattle and horses

Staphylococcus aureus (S. aureus) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for cattle and horses in previous scientific opinions. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9, and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR S. aureus can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (60-90% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 4 (Categories A, B and D; 1-5%, 5-10% and 10-33% probability of meeting the criteria, respectively) and the AHAW Panel was uncertain whether it meets the criteria in Sections 3 and 5 (Categories C and E, 33-90% and 60-90% probability of meeting the criteria, respectively). The animal species to be listed for AMR S. aureus according to Article 8 criteria include mainly mammals, birds, reptiles and fish.

Investigation of many bacterial and viral infections circulating in pigeons showing nervous symptoms

Pigeon’s flocks have shown several neurological symptoms including circling, torticollis, tremors, paralysis, which caused suspicion for viral or bacterial natural infections. Pigeon paramyxovirus type-1 (PPMV-1) is a notifiable disease-causing high morbidity and mortality with severe nervous symptoms. Clinical represented tissue specimens were collected from 50 infected pigeon flocks in eight governorates. All samples were examined bacteriologically (isolation, identification and serotyping) for E. coli, Salmonella spp., S. aureus and pseudomonas aeruginosa. Antimicrobial susceptibility test (AST) was accomplished for all isolates using a disk-diffusion test. For viral identification, RT-PCR specific oligonucleotide primers were used for distinguishing of Avian influenza virus, PPMV-1 and PPMV-3. Neurological manifestations were observed in pigeon’s flocks mainly in winter and autumn. The mortality rate in eight governorates was about 50% in 10 flocks and other houses mortality rate was ranged from 10 to 20%. Post mortem examination have shown hemorrhagic enteritis, soft and friable brain tissues and/or hemorrhages. The percentage of isolated bacteria E. coli, Salmonella spp., S. aureus and Pseudomonas aeruginosa were 75%, 75%, 50% and 18.75%; respectively. The antibiotic resistance pattern for bacterial isolates showed resist to ampicillin, amoxicillin- clavulinic acid, teteracyclin, ceftriaxone, doxycycline, sulfamethoxazole-trimethoprim and ceftazidine with different result for each type of bacteria, while Salmonella spp., isolates showed only a highly intermediate result for ciprofloxacin. Eight samples are positive with 16% to PPMV-1. Also, sample No.5,6,9 was co-infected with different types of bacterial isolates in addition to NDV. In conclusion, we reported several neurological symptoms in pigeon’s flocks mainly of bacterial infections (E. coli, Salmonella spp., S. aureus and Pseudomonas aeruginosa).