RESUMEN
To understand the relationship between changes in aroma and bacteria in pigeon breast meat (PBM) during preservation, bacterial communities and volatile compounds in PBM were analyzed using high-throughput sequencing and gas chromatography-ion mobility spectrometry. Analyses of total viable bacteria counts revealed that modified atmospheric packaging (MAP) and electron beam irradiation (EBI) could be used to extend the shelf-life of PBM to 10 d and 15 d, respectively. Furthermore, Lactococcus spp. and Psychrobacter spp. were the dominant bacterial genera of the MAP and EBI groups, respectively. The results of the study revealed 91 volatile organic compounds, one of which, butanal, was the most intense volatile organic compound while being an important source of aroma differences between the physical preservation techniques. Alpha-terpinolene, acetoin-M, gamma-butyrolactone, 1-hexanol-M, and 2,6-dimethyl-4-heptanone may be markers of PBM spoilage. During preservation, the MA group (treatment with 50 % CO2 + 50 % N2) demonstrated greater stabilization of PBM aroma. A Spearman correlation analysis showed that Lactococcus spp., Psychrobacter spp., and Pseudomonas spp. were the dominant bacterial genera of PBM during preservation and were closely related to an increase in the intensity of anisole, 2-methyl-3-furanthiol, and 5-methyl-2-furanmethanol, respectively. Lactococcus spp. and Psychrobacter spp. play crucial roles in the sensory degradation of PBM. In this study, we analyzed the changes in bacterial genera and volatile organic compounds of PBM under different physical preservation techniques to identify a suitable method for preserving PBM and evaluating its freshness.
Asunto(s)
Columbidae , Microbiología de Alimentos , Psychrobacter , Compuestos Orgánicos Volátiles , Compuestos Orgánicos Volátiles/análisis , Animales , Columbidae/microbiología , Psychrobacter/metabolismo , Odorantes/análisis , Conservación de Alimentos/métodos , Bacterias/clasificación , Carne/microbiología , Carne/análisis , Embalaje de Alimentos/métodos , Lactococcus , Cromatografía de Gases y Espectrometría de Masas , Aldehídos/análisis , MicrobiotaRESUMEN
Cryptococcosis is one of the major life-threatening opportunistic/systemic fungal diseases of worldwide occurrence, which can be asymptomatic or establish pneumonia and meningoencephalitis mainly in immunosuppressed patients, caused by the Cryptococcus neoformans and C. gattii species complexes. Acquisition is by inhaling fungal propagules from avian droppings, tree hollows and decaying wood, and the association of the molecular types with geographic origin, virulence and antifungal resistance have epidemiological importance. Since data on cryptococcosis in Alagoas are limited, we sought to determine the molecular types of etiological agents collected from clinical and environmental sources. We evaluated 21 isolates previously collected from cerebrospinal fluid and from environment sources (pigeon droppings and tree hollows) in Maceió-Alagoas (Brazil). Restriction fragment length polymorphism of URA5 gene was performed to characterize among the eight standard molecular types (VNI-VNIV and VGI-VGIV). Among isolates, 66.67% (14) were assigned to C. neoformans VNI - 12 of them (12/14) recovered from liquor and 2 from a tree hollow (2/14). One isolate from pigeon droppings (4.76%) corresponded to C. neoformans VNIV, while five strains from tree hollows and one from pigeon droppings (6, 28.57%) to C. gattii VGII. VNI-type was present in clinical and environmental samples and most C. neoformans infections were observed in HIV-positive patients, while types VNIV and VGII were prevalent in environmental sources in Alagoas. This is the first molecular characterization of Cryptococcus spp. in Alagoas, our study provides additional information on the ecoepidemiology of Cryptococcus spp. in Brazil, contributing to a closer view of the endemic species.
Asunto(s)
Columbidae , Criptococosis , Cryptococcus gattii , Cryptococcus neoformans , Microbiología Ambiental , Cryptococcus neoformans/genética , Cryptococcus neoformans/aislamiento & purificación , Cryptococcus neoformans/clasificación , Brasil/epidemiología , Criptococosis/microbiología , Criptococosis/epidemiología , Cryptococcus gattii/genética , Cryptococcus gattii/aislamiento & purificación , Cryptococcus gattii/clasificación , Humanos , Animales , Columbidae/microbiología , Técnicas de Tipificación Micológica , Polimorfismo de Longitud del Fragmento de Restricción , Heces/microbiología , GenotipoRESUMEN
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 ß-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.
Asunto(s)
Infecciones por Escherichia coli , Escherichia coli , Animales , Humanos , Escherichia coli/genética , Columbidae/microbiología , Virulencia/genética , Filogenia , Farmacorresistencia Bacteriana/genética , Antibacterianos/farmacología , Infecciones por Escherichia coli/veterinaria , Infecciones por Escherichia coli/microbiología , Factores de Virulencia/genéticaRESUMEN
Pigeon excreta can cause environmental and public health issues, particularly in urban and public areas. They are reservoirs of several human pathogens including fungi, bacteria, and viruses. Epidemiological data of pathogenic and opportunistic yeasts in pigeon droppings in Chon Buri, one of the most reputable tourist cities of Thailand, are scarce. The present study aimed to identify yeasts in pigeon droppings by MALDI-TOF mass spectrometry, and to study their prevalence in Chon Buri, Thailand. A total of 200 pigeon fecal samples were collected randomly from all 11 districts of Chon Buri. A sum of 393 yeast-like colonies were isolated on Sabourand's dextrose agar and CHROMagar media. These isolates were further confirmed for their species by MALDI-TOF MS. Twenty-four yeast species belonging to 11 different genera were identified in pigeon fecal samples. Candida spp., predominantly C. krusei (14.32%), were the most prevalent yeast species. Other yeast species, including C. glabrata (12.73%), C. metapsilosis (11.93%), Lodderomyces elongisporus (10.87%), C. tropicalis (7.16%), C. albicans (5.83%), and Cryptococcus neoformans (4.77%) were identified. This study provides valuable epidemiological data and diversity of yeasts in pigeon droppings in Chon Buri, Thailand, and also supports the use of MALDI-TOF MS for yeast identification and epidemiological surveillance.
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Columbidae , Cryptococcus neoformans , Animales , Humanos , Columbidae/microbiología , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Prevalencia , Tailandia , Levaduras , Candida albicansRESUMEN
With the development of the pigeon industry in Qingdao, more attention is paid to scientific breeding and precise treatment. This study isolated and identified Escherichia coli from pigeons in Qingdao to determine their susceptibility to 18 antibiotics. The PCR method was used to detect the prevalence of Extended-Spectrum ß-Lactamase genes, carbapenem resistance genes, 16S rRNA methylase genes and plasmid-mediated colistin resistance genes in the isolates. The results showed that Escherichia coli isolated from pigeons in Qingdao were the most resistant to tetracycline, followed by ampicillin, conventional cyclosporines, quinolones, cephalosporins, and aminoglycosides. No isolates were found to be resistant to amikacin, meropenem, colistin, tigecycline, and fosfomycin. The resistance to some antibiotics (ampicillin, tetracycline, and florfenicol) and the muti-drug resistance of Escherichia coli from meat pigeons were both higher than those from homing and ornamental pigeons. A total of 24.8% of the isolates showed multi-drug resistance, especially triple-drug resistance. Two isolates were found to carry ESBLs resistance genes. Hopefully, this study will provide a certain scientific basis for the clinical medication of pigeon colibacillosis, helping to prevent antimicrobial resistance transmission of Escherichia coli among different host animals and humans and maintain public health safety in Qingdao.
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Columbidae , Farmacorresistencia Bacteriana , Infecciones por Escherichia coli , Escherichia coli , Animales , Antibacterianos/farmacología , China , Columbidae/microbiología , Farmacorresistencia Bacteriana/genética , Escherichia coli/efectos de los fármacos , Infecciones por Escherichia coli/epidemiología , Infecciones por Escherichia coli/veterinaria , Pruebas de Sensibilidad Microbiana , ARN Ribosómico 16S , beta-Lactamasas/genéticaRESUMEN
BACKGROUND: Domestic pigeons carry pathogens in their droppings, posing a potential public health problem. METHODS: The phenotypic and genotypic antimicrobial resistances of Staphylococcus aureus and Enterococcus faecium in the feces of urban pigeons near hospitals with intensive care units were measured. RESULTS: Twenty-nine samples showed Enterococcus growth, whereas one was positive for S. aureus. The S. aureus isolate was sensitive to the antibiotics tested via antibiogram, however resistance genes were identified. E. faecium isolates showed phenotypic resistance to gentamicin, erythromycin, and ciprofloxacin. CONCLUSIONS: Antimicrobial profiles harmful to health were demonstrated in bacterial pathogens isolated from the external environment of hospitals.
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Enterococcus faecium , Animales , Antibacterianos/farmacología , Columbidae/microbiología , Enterococcus faecium/genética , Hospitales , Pruebas de Sensibilidad Microbiana , Staphylococcus aureus/genéticaRESUMEN
Bacterial resistance is a public and one health problem. Free-living birds can be reservoirs of multidrug-resistant bacteria and resistance genes. This study aimed to characterize the antimicrobial resistance of Escherichia coli isolated from free-living urban pigeons (Columba livia) in South Brazil. Ninety-two animals were sampled, and one isolate was obtained from each one. The isolates were characterized, and the antimicrobial resistance profile and beta-lactam and colistin resistance genes were investigated. The isolates were classified as phylogroups B1 (35%), B2 (33%), A (16%) and D (16%), and 14% of the strains had the eae virulence gene. All isolates were resistant to at least one antimicrobial, and 63% of them were multidrug-resistant. Geographical location where the pigeons were captured and presence of the eae gene were associated with multidrug resistance. blaVIM and mcr-1 genes were detected in one and two isolates, respectively. This is the first report of these genes in E. coli of pigeons. The blaVIM -positive isolate was classified as Shiga toxin-producing E. coli, and the isolates with mcr-1 were classified as Enterohaemorrhagic E. coli and Enteropathogenic E. coli, which raise additional concerns related to public health since these are zoonotic pathotypes. The results reveal that pigeons carry multidrug-resistant pathogenic E. coli, which may interest public health. Nonetheless, further studies on whether these animals are sources of contamination for humans must be performed to understand their role in spreading antimicrobial resistance.
Asunto(s)
Antiinfecciosos , Escherichia coli Enteropatógena , Infecciones por Escherichia coli , Proteínas de Escherichia coli , Animales , Antibacterianos/farmacología , Columbidae/microbiología , Infecciones por Escherichia coli/epidemiología , Infecciones por Escherichia coli/microbiología , Infecciones por Escherichia coli/veterinaria , Proteínas de Escherichia coli/genética , Humanos , Pruebas de Sensibilidad Microbiana/veterinariaRESUMEN
BACKGROUND: Escherichia coli is a bacterial species widely distributed among mammals and avian species, and also a member of the normal intestinal microbiota. However, some E. coli strains of different pathotypes can cause disease in both humans and animals. Atypical enteropathogenic E. coli (aEPEC) can infect both animals and humans or influence the severity of other ongoing infections. RESULTS: In the present study, a total of 332 samples were collected from ducks, geese, turkeys, chickens, and pigeons from the Hungarian Veterinary Diagnostic Directorate, two slaughterhouses, two pigeon keepers and one backyard chicken farm. E. coli was isolated and verified from 319 samples. The isolates were screened by PCR for diarrheagenic E. coli pathotypes. Altogether seven atypical enteropathogenic E. coli (aEPEC) strains were identified: two from four-week-old dead turkeys, two from force-fed geese, and three from pigeons. No further pathotypes were identified in the collection. The atypical EPEC strains were classified phylogenetically to B1, B2, and F, and four out of the seven aEPEC isolates proved to be multidrug resistant. Serotypes of aEPEC strains were uniform collected from same farms and showed diversity between their origins with O76, O145, O109 serogroups. CONCLUSIONS: This is the first report in the literature about aEPEC in goose (Anser anser domestica). Furthermore, this is the first isolation of aEPEC from turkeys and pigeons in Hungary. The uneven distribution of aEPEC in different age groups of poultry suggests that aEPEC disappears with growing up, but stress (e.g.: force-feeding) and concurrent diseases might promote its reappearance in the intestine.
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Columbidae/microbiología , Escherichia coli Enteropatógena/aislamiento & purificación , Aves de Corral/microbiología , Envejecimiento , Animales , Escherichia coli Enteropatógena/genética , Gansos/microbiología , Genotipo , Hungría , Pavos/microbiologíaRESUMEN
Campylobacter spp., such as Campylobacter jejuni and Campylobacter coli, are important zoonotic Gram-negative pathogens that cause acute intestinal diseases in humans. The optrA gene, encoding an ATP-binding cassette F (ABC-F) protein that confers resistance to oxazolidinones and phenicols, has been found in C. coli in China. In this study, the optrA gene was first identified in C. jejuni collected from retail meat in China from 2013 to 2016. Nine strains, isolated from a pigeon meat sample, carry the optrA gene. The molecular characteristics of the optrA-positive strains were determined by whole genome sequencing. Pulsed-field gel electrophoresis, multilocus sequence typing, and single nucleotide polymorphism analyses demonstrated that the nine optrA-positive isolates were genetically homogeneous. Phylogenetic characteristics and sequence comparison revealed that optrA was located on a chromosome-borne multidrug resistance genomic island. The optrA gene along with the tet(O) gene formed two different translocatable units (TUs), thereby supporting the transmission of TU-associated resistance genes. The emergence and spread of such TUs and strains are of great concern in terms of food safety, and measures must be implemented to avoid their dissemination in other Gram-negative bacteria and food chains.
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Campylobacter jejuni , Columbidae , Resistencia a Múltiples Medicamentos , Islas Genómicas , Carne , Animales , Antibacterianos/farmacología , Campylobacter jejuni/efectos de los fármacos , Campylobacter jejuni/genética , Columbidae/microbiología , Farmacorresistencia Bacteriana/genética , Resistencia a Múltiples Medicamentos/genética , Islas Genómicas/genética , Humanos , Carne/microbiología , Pruebas de Sensibilidad Microbiana , FilogeniaRESUMEN
Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed that the recently released DNA Prep library preparation kit, formerly known as Nextera Flex, overcomes some of these limitations. This study aimed to assess bias in coverage, tagmentation, GC content, average fragment size distribution, and de novo assembly quality using both the Nextera XT and DNA Prep kits from Illumina. When performing whole-genome sequencing on Escherichia coli and where coverage bias is the main concern, the DNA Prep kit may provide higher quality results; though de novo assembly quality, tagmentation bias and GC content related bias are unlikely to improve. Based on these results, laboratories with existing workflows based on Nextera XT would see minor benefits in transitioning to the DNA Prep kit if they were primarily studying organisms with neutral GC content.
Asunto(s)
Composición de Base , ADN Bacteriano/genética , Escherichia coli/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Animales , Columbidae/microbiología , Escherichia coli/aislamiento & purificación , Spheniscidae/microbiología , Secuenciación Completa del GenomaRESUMEN
Avian mycobacteriosis is an important disease of birds and is most often caused by Mycobacterium avium or Mycobacterium genavense. However, little information on the hematologic changes associated with this infectious disease in pigeons has been published. The aim of this investigation was to compare the hematologic parameters of domestic pigeons (Columba livia var. domestica) naturally infected with M avium subsp. avium (MAA) with clinically healthy pigeons. Blood samples were collected from 12 pigeons with suspected mycobacteriosis and 12 clinically healthy pigeons. All the birds with suspect infections were necropsied, and affected organs were cultured and examined on histopathology for mycobacteriosis. Total leukocyte and erythrocyte counts were performed on each blood sample with the Natt and Herrick method using a Neubauer hemocytometer. White blood cell (WBC) differential counts were performed on Giemsa-stained blood smears. Packed cell volumes (PCVs) were measured using the microhematocrit technique. Hemoglobin concentrations were measured with a spectrophotometer using the cyanomethemoglubin method. Mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentrations (MCHCs), and mean cell volumes (MCVs) were calculated manually. All of the infected birds had typical histopathologic findings of avian mycobacteriosis, which were confirmed using microbiologic and molecular methods to detect MAA. The hematologic data from the two groups were compared. The total WBC, heterophil, lymphocyte, and monocyte counts were significantly higher, and the PCV, HGB, MCH, and MCHC values were significantly lower in the infected birds compared with the clinically healthy pigeons.
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Columbidae , Mycobacterium , Tuberculosis Aviar , Animales , Columbidae/microbiología , Mycobacterium/aislamiento & purificación , Mycobacterium aviumRESUMEN
A total of 250 droppings of tumbler pigeons (Columba livia domestica, Columbidae) were collected individually from different breeders in Turkey, to investigate the presence and genotyping of microsporidian species by nested PCR and to reveal their zoonotic potential. In the present study, Enterocytozoon bieneusi was the only microsporidian species identified in 35 pigeons with an overall molecular prevalence of 14.0%. Only one known genotype zoonotic Peru6 was identified in all positive samples according to the sequence analyses of the internal transcribed spacer region of ribosomal DNA of E. bieneusi. This study represents the first report of E. bieneusi in pigeons in Turkey. Our study also confirms the competence of breeding pigeons as hosts for the zoonotic Peru6 genotype, corroborating its potential role as a source of human infection and environmental contamination. LAY SUMMARY: Microsporidia are spore-producing fungi defined as emerging opportunistic pathogens of humans. The occurrence of microsporidia in animals could be risky for human public health. Home kept breeding pigeons pose a high risk for transmission of the microsporidians to humans.
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Columbidae/microbiología , Enterocytozoon/genética , Heces/microbiología , Genotipo , Microsporidiosis/epidemiología , Filogenia , Zoonosis/epidemiología , Animales , Variación Genética , Prevalencia , Análisis de Secuencia de ADN , Turquía/epidemiologíaRESUMEN
OBJECTIVES: The overall aim was to determine whether gut bacteria of Columbia livia are a potential source of antitumour molecules. METHODS: Faecal and gut microbiota of Columbia livia were isolated, identified and conditioned media were prepared containing metabolites. Growth inhibition, lactate dehydrogenase cytotoxicity and cell survival assays were accomplished against cervical cancer cells. Next, liquid-chromatography mass spectrometry was conducted to elucidate the molecules present. RESULTS: A plethora of bacteria from faecal matter and gastrointestinal tract were isolated. Selected conditioned media exhibited potent anticancer effects and displayed cytotoxicity to cervical cancer cells at IC50 concentration of 10.65 and 15.19 µg/ml. Moreover, cells treated with conditioned media exhibited morphological changes, including cell shrinking and rounding; indicative of apoptosis, when compared to untreated cells. A total of 111 and 71 molecules were revealed from these gut and faecal metabolites. The identity of 60 molecules were revealed including, dihydroxymelphalan. Nonetheless, 122 molecules remain unidentified and are the subject of future studies. CONCLUSION: These findings suggest that gut bacteria of Columbia livia possess molecules, which may have anticancer activities. Further in silico testing and/or high throughput screening will determine potential anticancer properties of these molecules.
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Asunto(s)
Proliferación Celular/efectos de los fármacos , Columbidae/microbiología , Medios de Cultivo Condicionados/farmacología , Microbioma Gastrointestinal/fisiología , Animales , Antineoplásicos/farmacología , Bacterias/química , Medios de Cultivo Condicionados/química , Descubrimiento de Drogas , Células HaCaT , Células HeLa , Humanos , Concentración 50 Inhibidora , Células MCF-7 , Melfalán/aislamiento & purificación , Células PC-3RESUMEN
Previously, a fungus was isolated from a diseased pigeon group clinically suspected of being infected with Candida. The fungus was subsequently identified as Candida glabrata using morphology, physiology, biochemistry, and molecular biology testing methods. In the present study, to determine the controlling effects of Chinese herbal medicine for C. glabrata, the bacteriostatic effects of the ethanol extracts Acorus gramineus, Sophora flavescens, Polygonum hydropiper, Cassia obtusifolia, Pulsatilla chinensis, Dandelion, and Cortex phellodendri on C. glabrata in vitro were analyzed. The results showed that the minimum inhibitory concentrations (MIC80) of Cortex phellodendri was 0.25 µg/µL. Meanwhile, that of S. flavescens was 32 µg/µL; C. obtusifolia was 56 µg/µL; A. gramineus and Polygonum hydropiper was 64 µg/µL; and P. chinensis was 112 µg/µL. However, MIC80 for Dandelion was undetectable. In addition, improved drug sensitivity tests revealed that colonies had grown after 24 h in the blank group, as well as the Polygonum hydropiper, P. chinensis, Dandelion, and ethanol groups. The colonies first appeared at the 48-hour point in the other drug-sensitive medium of Chinese herbal medicine. However, no colony growth was found in Cortex phellodendri medium, and the formation of the maximum colony diameter in that group was later than the blank group (e.g., 96 h in the blank group and 120 h in the Chinese herbal medicine group). It was observed that only 17 colony-forming units had grown in 125 µg/µL of the S. flavescens medium, which was significantly different from other groups. Also, the final colony diameter was significantly smaller than that of the other experimental groups. Therefore, it was determined that the A. gramineus, S. flavescens, Polygonum hydropiper, Cassia obtusifolia, P. chinensis, and Cortex phellodendri had certain inhibitory effects on the growth of the C. glabrata. Among those, it was observed that the Cortex phellodendri had the strongest inhibitory effects, followed by the S. flavescens. In the future, these Chinese herbal medicines are expected to be used to treat the fungal infections related to C. glabrata in poultry to improve production performance.
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Candida glabrata , Medicamentos Herbarios Chinos , Animales , Antibacterianos/farmacología , Enfermedades de las Aves/tratamiento farmacológico , Enfermedades de las Aves/microbiología , Candida glabrata/clasificación , Candida glabrata/efectos de los fármacos , Candida glabrata/aislamiento & purificación , Columbidae/microbiología , Medicamentos Herbarios Chinos/farmacología , Pruebas de Sensibilidad Microbiana/veterinariaRESUMEN
Species-specific detection of Chlamydia psittaci is challenging and all published PCR tests have so far shown deficiencies in specificity or sensitivity. The present investigation reports on the development of a species-specific real-time PCR assay for C. psittaci. The test is based on an 84 bp indel in a gene of unknown function that is unique to C. psittaci. The Cps-indel84-PCR assay was validated on a wide range of chlamydial and other bacterial strains as well as on clinical samples from animals and humans in two different diagnostic laboratories in Germany and Denmark. Furthermore, the test was employed for investigating samples from racing pigeon flocks in Denmark. The evaluation showed that the Cps-indel84-PCR assay has excellent test characteristics and is a highly reliable method for identifying C. psittaci in clinical samples both from humans and animals.
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Enfermedades de las Aves/microbiología , Infecciones por Chlamydia/veterinaria , Chlamydophila psittaci/genética , Columbidae/microbiología , Reacción en Cadena en Tiempo Real de la Polimerasa/veterinaria , Animales , Enfermedades de las Aves/diagnóstico , Enfermedades de las Aves/epidemiología , Infecciones por Chlamydia/diagnóstico , Infecciones por Chlamydia/epidemiología , Infecciones por Chlamydia/microbiología , Dinamarca/epidemiología , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Especificidad de la EspecieRESUMEN
In 2018, a cluster of two cases of cryptococcosis occurred at the Queen Elizabeth University Hospital (QEUH) in Glasgow, Scotland (UK). It was postulated that these cases may have been linked to pigeon droppings found on the hospital site, given there have been previous reports of Cryptococcus neoformans associated with pigeon guano. Although some samples of pigeon guano taken from the site yielded culturable yeast from genera related to Cryptococcus, they have since been classified as Naganishia or Papiliotrema spp., and no isolates of C. neoformans were recovered from either the guano or subsequent widespread air sampling. In an attempt to further elucidate any possible shared source of the clinical isolates, we used whole-genome sequencing and phylogenetic analysis to examine the relationship of the two Cryptococcus isolates from the QEUH cases, along with two isolates from sporadic cases treated at a different Glasgow hospital earlier in 2018. Our work demonstrated that these four clinical isolates were not clonally related; while all isolates were from the VNI global lineage and of the same mating type (MATα), the genotypes of the two QEUH isolates were separated by 1885 base changes and belonged to different sub-lineages, recently described as the intercontinental sub-clades VNIa-93 and VNIa-5. In contrast, one of the two sporadic 2018 clinical isolates was determined to belong to the VNIb sub-lineage and the other classified as a VNIV/VNI hybrid. Our work demonstrated that the two 2018 QEUH isolates and the two prior C. neoformans clinical isolates were all genetically distinct. It was not possible to determine whether the QEUH genotypes stemmed from independent sources or from the same source, i.e. pigeons carrying different genotypes, but it should be noted that whilst members of allied genera within the Tremellomycetes were isolated from the hospital environment, there were no environmental isolations of C. neoformans.
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Criptococosis/microbiología , Cryptococcus neoformans/genética , Cryptococcus neoformans/aislamiento & purificación , Anciano , Animales , Niño , Columbidae/microbiología , Cryptococcus neoformans/clasificación , Heces/microbiología , Femenino , Genoma Fúngico , Genómica , Genotipo , Humanos , Masculino , Filogenia , EscociaRESUMEN
Although cryptococcosis is widely recognized as infection by Cryptococcus neoformans sensu lato from environmental sources, information concerning the characteristics of environmental isolates of C. neoformans s. l. and how they are related to clinical isolates is very limited, especially in East China. In this study, 61 environmental isolates of C. neoformans were recovered from pigeon (Columba livia) droppings from the Yangtze River Delta region of East China. These isolates were genotyped using the ISHAM-MLST consensus scheme and their antifungal drug susceptibilities were determined following the CLSI M27-A3 guidelines. The 61 isolates were found belonging to 13 sequence types (STs), including several novel STs such as ST254 and ST194. The dominant ST in this environmental sample was ST31, different from that of clinical strains (ST5) in this region. Azole-resistance, such as fluconazole (FLU)-resistance, was observed among our environmental C. neoformans isolates. The findings of this study expand our understanding of ecological niches, population genetic diversity, and azole-resistance characteristics of the yeast in East China. Our research lays the foundation for further comparative analysis the potential mechanisms for the observed differences between environmental and clinical populations of C. neoformans in China. LAY SUMMARY: Cryptococcosis is widely recognized as infection by Cryptococcus neoformans sensu lato from environmental sources. However, there is currently limited information about the genetic diversity and antifungal susceptibility of environmental C. neoformans s. l. isolates, including how they may differ from clinical samples. In this study, we collected 61 environmental C. neoformans isolates from domestic pigeon droppings from the Yangtze River Delta region of East China. These isolates were genotyped using multi-locus sequencing. We found a high genotypic diversity in this population of C. neoformans, with several novel genotypes and a distribution of genotypes different from that of clinical strains in this region. Azole-resistance, such as fluconazole (FLU)-resistance, was observed among our environmental C. neoformans isolates. The findings of this study expand our understanding of ecological niches, genetic diversity, and azole-resistance characteristics of the yeast in East China. Our research lays the foundation for phylogenomic analysis investigating why and how disparate population structures of C. neoformans isolates formed between environmental and clinical sources in the region.
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Antifúngicos/farmacología , Cryptococcus neoformans/efectos de los fármacos , Microbiología Ambiental , Variación Genética , Genotipo , Animales , China , Columbidae/microbiología , Criptococosis/microbiología , Cryptococcus neoformans/clasificación , Cryptococcus neoformans/aislamiento & purificación , Farmacorresistencia Fúngica , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Técnicas de Tipificación Micológica , Filogenia , Ríos/microbiologíaRESUMEN
Pigeons, as the only altricial birds in poultry, are the primary Trichomonas gallinae (T. gallinae) host. To study the effects of T. gallinae infection on gut microbiota, we compared the microbiota diversity and composition in gastrointestinal (GI) tracts of pigeons at the age of 14 and 21 day with different degrees of T. gallinae infection. Thirty-six nestling pigeons were divided into three groups: the healthy group, low-grade and high-grade trichomonosis group. Then, the crop, small intestine and rectum contents were obtained for sequencing of the 16S rRNA gene V3-V4 hypervariable region. The results showed that the microbiota diversity was higher in crop than in small intestine and rectum, and the abundance of Lactobacillus genus was dominant in small intestine and rectum of healthy pigeons at 21 days. T. gallinae infection decreased the microbiota richness in crop at 14 days. The abundance of the Firmicutes phylum and Lactobacillus genus in small intestine of birds at 21 days were decreased by infection, however the abundances of Proteobacteria phylum and Enterococcus, Atopobium, Roseburia, Aeriscardovia and Peptostreptococcus genus increased. The above results indicated that crop had the highest microbiota diversity among GI tract of pigeons, and the gut microbiota diversity and composition of pigeon squabs were altered by T. gallinae infection.
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Columbidae/microbiología , Columbidae/parasitología , Microbioma Gastrointestinal/genética , Microbioma Gastrointestinal/fisiología , Trichomonas/parasitología , Animales , Enfermedades de las Aves/microbiología , Enfermedades de las Aves/parasitología , Firmicutes/genética , Genotipo , Lactobacillus/genética , Filogenia , ARN Ribosómico 16S/genética , Tricomoniasis/microbiología , Tricomoniasis/parasitologíaRESUMEN
Lactobacillus species play an important role in the host and although they are non-pathogenic, they could act as reservoirs for antibiotic resistance genes, with the potential risk of transfer to other bacteria inhabiting the gastrointestinal tract. The aim of this study was to identify Lactobacillus species derived from feces of domesticated pigeons and to characterize their phenotypic and genotypic antimicrobial resistance (AMR) profiles. A total of 57 Lactobacillus isolates were classified into six species using the MALDI-TOF technique and 16S rDNA restriction analysis. Strains of L. ingluviei (31%), L. salivarius (28%) and L. agilis (23%) were the dominant species isolated. Determination of antimicrobial susceptibility by the microdilution broth method showed widespread resistance to kanamycin (89%), tetracycline (84%), streptomycin (63%), and enrofloxacin (37%). Less than 30% of the isolates were resistant to erythromycin, lincosamides, gentamycin, chloramphenicol and vancomycin. Over half (51%) of the lactobacilli were classified as multidrug resistant. Tet genes were detected in 79% of isolates; the lnuA, cat, ermB, ermC, ant(6)-Ia, ant(4')-Ia, and int-Tn genes were found at a lower frequency. Sequence analysis of the quinolone resistance-determining region (QRDR)of the gyrA gene showed that fluoroquinolone resistance in lactobacilli was the result of a mutation that lead to a change in the amino acid sequence (Ser83âTyr/Leu/Phe). Domesticated pigeons could be a reservoir for AMR Lactobacillus strains and AMR genes.
Asunto(s)
Antibacterianos/farmacología , Columbidae/microbiología , Farmacorresistencia Bacteriana , Heces/microbiología , Lactobacillus/clasificación , Lactobacillus/efectos de los fármacos , Lactobacillus/genética , Sustitución de Aminoácidos , Animales , Genes Bacterianos , Genotipo , Lactobacillus/aislamiento & purificación , Pruebas de Sensibilidad Microbiana , Tipificación Molecular , Mutación , Fenotipo , Polonia , ARN Ribosómico 16S/genética , Espectrometría de Masa por Láser de Matriz Asistida de Ionización DesorciónRESUMEN
Globally, gulls have been associated with carriage of high levels of Escherichia coli strains resistant to critically important antimicrobials (CIAs), a major concern, as these antimicrobials are the sole alternative or one among only a few alternatives available to treat severe life-threatening infections in humans. Previous studies of Australian silver gulls demonstrated high levels of resistance to CIAs, particularly fluoroquinolone and extended-spectrum cephalosporins, among E. coli strains (carriage at 24% and 22%, respectively). This study aimed to identify and characterize strains from four distinct bird species inhabiting a common coastal environment, determine the frequency of carriage of CIA-resistant E. coli strains, and examine if these resistant clones and their resistance-encoding mobile genetic elements (MGEs) could be transmitted between species. CIA-resistant E. coli was detected in silver gulls (53%), little penguins (11%), and feral pigeons (10%), but not in bridled terns. In total, 37 different sequence types (STs) were identified, including clinically significant human-associated lineages, such as ST131, ST95, ST648, ST69, ST540, ST93, ST450, and ST10. Five main mobile genetic elements associated with blaCTX-M-positive E. coli strains isolated from three bird species were detected. Examination of clonal lineages and MGEs provided indirect evidence of transfer of resistance between bird species. The carriage of CIA-resistant E. coli by gulls and pigeons with proximity to humans, and in some instances food-producing animals, increases the likelihood of further bidirectional dissemination.IMPORTANCE It has been shown that 20% of Australian silver gulls carry drug-resistant Escherichia coli strains of anthropogenic origin associated with severe diseases, such as sepsis and urinary tract infections, in humans. To further characterize the dynamics of drug-resistant E. coli in wildlife populations, we investigated the carriage of critically important antimicrobial (CIA) drug-resistant E. coli in four bird species in a common environment. Our results indicated that gulls, pigeons, and penguins carried drug-resistant E. coli strains, and analysis of mobile genetic elements associated with resistance genes indicated interspecies resistance transfer. Terns, representing a bird species that forages on natural food sources at sea and distant from humans, did not test positive for drug-resistant E. coli This study demonstrates carriage of CIA-resistant bacteria in multiple bird species living in areas commonly inhabited by humans and provides further evidence for a leapfrog effect of resistance in wildlife, facilitated by feeding habits.