The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

A real-time reverse transcriptase PCR (RRT-PCR) assay based on the avian influenza virus matrix gene was developed for the rapid detection of type A influenza virus. Additionally, H5 and H7 hemagglutinin subtype-specific probe sets were developed based on North American avian influenza virus sequences. The RRT-PCR assay utilizes a one-step RT-PCR protocol and fluorogenic hydrolysis type probes. The matrix gene RRT-PCR assay has a detection limit of 10 fg or approximately 1,000 copies of target RNA and can detect 0.1 50% egg infective dose of virus. The H5- and H7-specific probe sets each have a detection limit of 100 fg of target RNA or approximately 103 to 104 gene copies. The sensitivity and specificity of the real-time PCR assay were directly compared with those of the current standard for detection of influenza virus: virus isolation (VI) in embryonated chicken eggs and hemagglutinin subtyping by hemagglutination inhibition (HI) assay. The comparison was performed with 1,550 tracheal and cloacal swabs from various avian species and environmental swabs obtained from live-bird markets in New York and New Jersey. Influenza virus-specific RRT-PCR results correlated with VI results for 89% of the samples. The remaining samples were positive with only one detection method. Overall the sensitivity and specificity of the H7- and H5-specific RRT-PCR were similar to those of VI and HI.

Development of a Real-Time Reverse Transcriptase PCR Assay for Type A Influenza Virus and the Avian H5 and H7 Hemagglutinin Subtypes

Highly pathogenic avian influenza A viruses of subtypes H5 and H7 are the causative agents of fowl plague in poultry. Influenza A viruses of subtype H5N1 also caused severe respiratory disease in humans in Hong Kong in 1997 and 2003, including at least seven fatal cases, posing a serious human pandemic threat. Between the end of February and the end of May 2003, a fowl plague outbreak occurred in The Netherlands. A highly pathogenic avian influenza A virus of subtype H7N7, closely related to low pathogenic virus isolates obtained from wild ducks, was isolated from chickens. The same virus was detected subsequently in 86 humans who handled affected poultry and in three of their family members. Of these 89 patients, 78 presented with conjunctivitis, 5 presented with conjunctivitis and influenza-like illness, 2 presented with influenza-like illness, and 4 did not fit the case definitions. Influenza-like illnesses were generally mild, but a fatal case of pneumonia in combination with acute respiratory distress syndrome occurred also. Most virus isolates obtained from humans, including probable secondary cases, had not accumulated significant mutations. However, the virus isolated from the fatal case displayed 14 amino acid substitutions, some of which may be associated with enhanced disease in this case. Because H7N7 viruses have caused disease in mammals, including horses, seals, and humans, on several occasions in the past, they may be unusual in their zoonotic potential and, thus, form a pandemic threat to humans.

https://www.pnas.org/content/pnas/101/5/1356.full.pdf

Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome

The global emergence of multidrug-resistant Gram-negative bacteria is a growing threat to antibiotic therapy. The chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. Multidrug pumps, particularly those represented by the clinically relevant AcrAB-TolC and Mex pumps of the resistance-nodulation-division (RND) superfamily, not only mediate intrinsic and acquired multidrug resistance (MDR) but also are involved in other functions, including the bacterial stress response and pathogenicity. Additionally, efflux pumps interact synergistically with other resistance mechanisms (e.g., with the outer membrane permeability barrier) to increase resistance levels. Since the discovery of RND pumps in the early 1990s, remarkable scientific and technological advances have allowed for an in-depth understanding of the structural and biochemical basis, substrate profiles, molecular regulation, and inhibition of MDR pumps. However, the development of clinically useful efflux pump inhibitors and/or new antibiotics that can bypass pump effects continues to be a challenge. Plasmid-borne efflux pump genes (including those for RND pumps) have increasingly been identified. This article highlights the recent progress obtained for organisms of clinical significance, together with methodological considerations for the characterization of MDR pumps.

/pdf/the-challenge-of-efflux-mediated-antibiotic-resistance-in-3le37l35cs.pdf

The Challenge of Efflux-Mediated Antibiotic Resistance in Gram-Negative Bacteria

At the beginning of 2005, an outbreak of ceruminous otitis has been observed in a breeders flock belonging to the Robusta Lionata breed, a native chicken breed reared in a Centre for the valorisation and conservation of native poultry breeds. The disease caused a high morbidity rate (90% of birds), whereas the mortality affected only 10% of the birds. The death of the birds was preceded by clinical signs, such as worsening of the ceruminous otitis with abundant secretion of bad-smelling cerumen, lack of appetite and depression. The otitis externa, mainly bilateral, was the only evident finding at necropsy. Laboratory examinations showed only the presence of Mycoplasma synoviae, either by isolation on culture media or by PCR, on ear and choana samples. Aspergillus fumigatus was detected only in one bird. In this paper, the Authors report for the first time on an outbreak of ceruminous otitis in native chicken breeds and point out that the only pathogenic agent isolated from the birds has been Mycoplasma synoviae.

Ceruminous otitis in native chicken breeders belonging to Robusta Lionata breed

This study analyzed data on the sources and the level of Italians’ awareness on the risk of infection by SARS-CoV-2 at the human–animal interface. Data were collected through a survey-type investigation on a representative sample of the Italian population. Forty-five percent of the interviewees were aware that companion animals could be infected by SARS-CoV-2. However, 29.8% were familiar with preventive measures to adopt to avoid viral transmission between infected humans and companion animals, and only 20.7% knew which companion animals could be at risk of infection. Higher awareness regarding the risk of SARS-CoV-2 transmission between animals and humans (51.7%) and the measures to prevent it (33.3%) was detected among companion animals’ owners. Notably, 40.4% of interviewees were not informed at all. Television broadcasts (26.4%) represented the main source of information, while only 3.5% of the interviewees relied on veterinarians, of which 31.9% considered this source of information as the most trustworthy. Overall, 72.4% of Italians recognized that the communication campaign on COVID-19 and companion animals was inadequate. This survey highlights the need for increasing the public awareness of the risk of companion animals being infected with SARS-CoV-2 and the involvement of professionals in the public communication on zoonoses.

/pdf/sars-cov-2-and-companion-animals-sources-of-information-and-2uqa7v41.pdf

SARS-CoV-2 and Companion Animals: Sources of Information and Communication Campaign during the COVID-19 Pandemic in Italy

Antimicrobial Resistance Dynamics in the Chicken Gut after Amoxicillin and Thiamphenicol Treatments

M. DRIGOa, G. RIBAUDOb, A. PICCIRILLOc, D. PASOTTOa, V. PAVANb, M.L. MENANDROa, M. GIACOMELLIc, M. DALLA BONAc, C. MONTESISSAc, G. ZAGOTTOb a Dipartimento di Medicina Animale, Produzioni e Salute (MAPS), Università degli Studi di Padova b Dipartimento di Scienze del Farmaco, Università degli Studi di Padova c Dipartimento di Biomedicina Comparata e Alimentazione (BCA), Università degli Studi di Padova

Qualità microbiologica e chimico-fisica dell’acqua di abbeverata in allevamenti suini in Veneto

Gli Autori riportano i risultati di un’indagine preliminare che aveva lo scopo di far adattare alle condizioni di vita naturale starne Perdix perdix provenienti da un allevamento intensivo, nella Zona di Ripopolamento e Cattura di“Serre-Persano” (SA). Nel corso dell’indagine e stato valutato anche lo stato sanitario degli animali. Le starne, dopo aver sostato per circa 2 settimane nel parchetto di ambientamento sono state liberate progressivamente in gruppi di 4, a distanza di una settimana l’uno dall’altro. Al momento dell’arrivo, al rilascio ed alla cattura sono stati effettuati campionamenti individuali da sottoporre ad esami microbiologici. Nei due mesi di indagine non si e verificato alcun caso di mortalita nelle strutture di ambientamento, mentre il tasso di sopravvivenza fra gli animali rilasciati e stato del 58,3%. Gli animali hanno manifestato anche la tendenza a modificare i propri schemi comportamentali. Gli esami di laboratorio non hanno permesso l’isolamento di microrganismi di particolare rilievo. Questi risultati confermano la necessita di adoperare corretti sistemi di rilascio per migliorare la capacita di ambientamento e di sopravvivenza degli animali.

http://www.mountainecology.org/index.php/me/article/download/143/125

Alessandra Piccirillo

Papers

Ceruminous otitis in native chicken breeders belonging to Robusta Lionata breed

SARS-CoV-2 and Companion Animals: Sources of Information and Communication Campaign during the COVID-19 Pandemic in Italy

Antimicrobial Resistance Dynamics in the Chicken Gut after Amoxicillin and Thiamphenicol Treatments

Qualità microbiologica e chimico-fisica dell’acqua di abbeverata in allevamenti suini in Veneto

Indagine preliminare sull'ambientamento di starne allevate con metodi intensivi