[D-CBP study: Evaluation of lung cancer management times]. / Étude D-CBP : Évaluation des délais de prise en charge du cancer broncho- pulmonaire au sein du service de Pneumologie et d'Oncologie Thoracique du CHU de Caen.

INTRODUCTION: Lung cancer is the leading cause of cancer-related death. Delays may have an impact on patient survival. The objective of this study was to evaluate the diagnostic and therapeutic management times for patients admitted for lung cancer treatment in the Respiratory Department of CHU de Caen Normandie. MATERIALS AND METHODS: This is a retrospective, single-center and observational study, conducted on all patients treated for lung cancer from June 2017 to January 2018 in our department of pneumology in the Caen Normandie CHU. The main median times were investigated were: Global Time (abnormal imaging-treatment), Diagnosis time (abnormal imaging-diagnosis) and Treatment Time (diagnosis-treatment). RESULTS: One hundred and twenty-seven (127) patients were included. Median global time was 55.5 days [31,25; 393], median diagnosis time was 22 days [13; 49], and median treatment time was 24.5 days [12,25; 45]. DISCUSSION: Our treatment times are consistent with those previously published. Areas for improvement are being developed in accordance with the 2014-2019 cancer plan, in particularly the creation in our institution of a specific care pathway for patients with lung cancer.

Interaction of CP levels in maternal and nursery diets, and its effect on performance, protein digestibility, and serum urea levels in piglets.

Reduced protein levels in nursery diets have been associated with a lower risk of postweaning diarrhea, but the interaction with CP levels in maternal diet on the performance of the offspring remains unclear. The objective of this study was to determine the effect of protein content in sow gestation and piglet nursery diets on the performance of the piglets until slaughter. This was studied in a 2 × 2 factorial trial (35 sows, 209 piglets), with higher or lower (H or L) dietary CP in sow diets (168 vs 122 g CP/kg) during late gestation. A standard lactation feed was provided for all sows (160 g CP/kg). For both sow treatments, half of the litters received a higher or lower CP in the piglet nursery diet (210 vs 166 g CP/kg). This resulted in four possible treatment combinations: HH, HL, LH and LL, with sow treatment as first and piglet treatment as second letter. For each phase, all diets were iso-energetic and had a similar level of essential amino acids. Ps*p is the p-value for the interaction effect between sow and piglet treatment. In the nursery phase (3.5-9 weeks of age), a tendency toward interaction between piglet and sow treatments with feed efficiency (Ps*p = 0.08) was observed with HH having the highest gain:feed ratio (G:F) (0.74 ± 0.01), LH the lowest (0.70 ± 0.01) and the other two groups intermediate. In the growing-finishing phase, an interaction was observed between the piglet and sow diets with decreased G:F for LH (Ps*p = 0.04) and a tendency toward interaction with increased daily feed intake for LH (Ps*p = 0.07). The sow diet showed a tendency toward a long-lasting effect on the dressing percentage and meat thickness of the offspring, which was higher for the progeny of H sows (Ps < 0.01 and Ps = 0.02, respectively). At 23 weeks, serum urea concentrations tended to be lower for the HH and LL groups (Ps*p = 0.07). Fecal consistency scores were higher at day 10-day 14 after weaning for piglets from L sows (Ps = 0.03 and Ps < 0.01, respectively). At day 7 after weaning, fecal consistency score was higher for piglets fed the higher protein diet (Pp < 0.01). At 8 weeks of age, the apparent total tract digestibility of CP (ATTDCP) interacted between piglet and sow diet (Ps*p = 0.02), with HH showing the highest digestibility values. In conclusion, the protein levels in sow late-gestation and piglet nursery diets interacted with feed efficiency, ATTDCP and serum urea concentrations in the nursery phase.

On-farm comparisons of different cleaning protocols in broiler houses.

The present study evaluated the effectiveness of 4 cleaning protocols designed to reduce the bacteriological infection pressure on broiler farms and prevent food-borne zoonoses. Additionally, difficult to clean locations and possible sources of infection were identified. Cleaning and disinfection rounds were evaluated in 12 broiler houses on 5 farms through microbiological analyses and adenosine triphosphate hygiene monitoring. Samples were taken at 3 different times: before cleaning, after cleaning, and after disinfection. At each sampling time, swabs were taken from various locations for enumeration of the total aerobic flora and Enterococcus species pluralis ( SPP:). In addition, before cleaning and after disinfection, testing for Escherichia coli and Salmonella was carried out. Finally, adenosine triphosphate swabs and agar contact plates for total aerobic flora counts were taken after cleaning and disinfection, respectively. Total aerobic flora and Enterococcus spp. counts on the swab samples showed that cleaning protocols which were preceded by an overnight soaking with water caused a higher bacterial reduction compared to protocols without a preceding soaking step. Moreover, soaking of broiler houses leads to less water consumption and reduced working time during high pressure cleaning. No differences were found between protocols using cold or warm water during cleaning. Drinking cups, drain holes, and floor cracks were identified as critical locations for cleaning and disinfection in broiler houses.

Comparison of sampling procedures and microbiological and non-microbiological parameters to evaluate cleaning and disinfection in broiler houses.

Cleaning and disinfection of the broiler stable environment is an essential part of farm hygiene management. Adequate cleaning and disinfection is essential for prevention and control of animal diseases and zoonoses. The goal of this study was to shed light on the dynamics of microbiological and non-microbiological parameters during the successive steps of cleaning and disinfection and to select the most suitable sampling methods and parameters to evaluate cleaning and disinfection in broiler houses. The effectiveness of cleaning and disinfection protocols was measured in six broiler houses on two farms through visual inspection, adenosine triphosphate hygiene monitoring and microbiological analyses. Samples were taken at three time points: 1) before cleaning, 2) after cleaning, and 3) after disinfection. Before cleaning and after disinfection, air samples were taken in addition to agar contact plates and swab samples taken from various sampling points for enumeration of total aerobic flora, Enterococcus spp., and Escherichia coli and the detection of E. coli and Salmonella. After cleaning, air samples, swab samples, and adenosine triphosphate swabs were taken and a visual score was also assigned for each sampling point. The mean total aerobic flora determined by swab samples decreased from 7.7±1.4 to 5.7±1.2 log CFU/625 cm2 after cleaning and to 4.2±1.6 log CFU/625 cm2 after disinfection. Agar contact plates were used as the standard for evaluating cleaning and disinfection, but in this study they were found to be less suitable than swabs for enumeration. In addition to measuring total aerobic flora, Enterococcus spp. seemed to be a better hygiene indicator to evaluate cleaning and disinfection protocols than E. coli. All stables were Salmonella negative, but the detection of its indicator organism E. coli provided additional information for evaluating cleaning and disinfection protocols. Adenosine triphosphate analyses gave additional information about the hygiene level of the different sampling points.

Polyphasic characterization of Salmonella Enteritidis isolates on persistently contaminated layer farms during the implementation of a national control program with obligatory vaccination: a longitudinal study.

Since 2007, a national Salmonella control program including obligatory vaccination has been ongoing in Belgium. In this context, the aim of the present study was to investigate the diversity of Salmonella enterica serovar Enteritidis isolates on 5 persistently contaminated Belgian layer farms and to examine the potential sources and transmission routes of Salmonella Enteritidis contamination on the farms during successive laying rounds. A collection of 346 Salmonella isolates originating from the sampled farms were characterized using a combination of multilocus variable number of tandem repeat analysis (MLVA) and phage typing (PT). On each farm, one or 2 dominant MLVA-PT types were found during successive laying cycles. The dominant MLVA type was different for each of the individual farms, but some farms shared the same dominant phage type. Isolates recovered from hens' feces and ceca, egg contents, eggshells, vermin (mice, rats, red mites, and flies), and pets (dog and cat feces) had the same MLVA-PT type also found in the inside henhouse environment of the respective layer farm. Persistent types were identified in the layer farm inside environment (henhouse and egg collecting area). Furthermore, this study demonstrated cross-contamination of Salmonella between henhouses and between the henhouse and the egg collecting area. Additional isolates with a different MLVA-PT type were also recovered, mainly from the egg collecting area. A potential risk for cross-contamination of Salmonella between the individual layer farms and their egg trader was identified.

Persistent Salmonella Enteritidis environmental contamination on layer farms in the context of an implemented national control program with obligatory vaccination.

The aim of this study was to closely examine the Salmonella enterica serovar Enteritidis environmental contamination on persistently positive layer farms in Belgium during successive laying cycles. All of the farms were required to vaccinate their layers under the national control program for Salmonella. Seven farms with previous or current Salmonella Enteritidis contamination were monitored during different stages of the laying period and after cleaning and disinfection (CD). Environmental samples, including from the equipment and vermin, were taken in the henhouse and egg-collecting area. Dilutions were performed to define the degree of Salmonella Enteritidis contamination. Eggshells, egg contents, and ceca were also tested for Salmonella. At the end of the first sampled laying period, 41.6% of the environmental samples were contaminated with Salmonella Enteritidis. After CD, the prevalence dropped to 11.4%. On average, the prevalence in the second laying period increased again: 17.8, 18.4, and 22.3% at the onset, middle, and end of the lay period, respectively. After CD before the third laying period, the prevalence decreased to 6.6% and stabilized at the onset of lay (6.3%). During lay, as well as after CD, a wide variety of contaminated environmental samples were found; for example, in the henhouse, in the egg-collecting area, on mobile equipment and in or on vermin. In the henhouse during laying, the most recurrent and highly contaminated sites were the overshoes, floor, manure belt, and hen feces. The egg-collecting area had a significantly higher number of contaminated samples compared with that of the henhouse. For both sites, the floor appeared to be the most suitable sampling site to estimate the Salmonella Enteritidis status of the farms. Eggshell and egg content contamination varied between 0.18 and 1.8% and between 0.04 and 0.4%, respectively. In total, 2.2% of the analyzed ceca contained Salmonella Enteritidis. This study revealed that Salmonella Enteritidis is present in the environment of persistently Salmonella Enteritidis-contaminated layer farms, demonstrated that in many cases Salmonella Enteritidis contamination was not eliminated after CD, and identified the egg-collecting area as a critical point on most farms.

Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria.

Minimal standards for describing new taxa within the aerobic endospore-forming bacteria are proposed, following Recommendation 30b of the Bacteriological Code (1990 Revision). These minimal standards are recommended as guidelines to assist authors in the preparation of descriptions for novel taxa. They encourage broad polyphasic characterization and the construction of descriptions that are practically useful in routine diagnostic laboratories. The proposals have been endorsed by the Subcommittee on the Taxonomy of the Genus Bacillus and Related Organisms of the International Committee on Systematics of Prokaryotes.

Identification of lactobacilli isolated from the cloaca and vagina of laying hens and characterization for potential use as probiotics to control Salmonella Enteritidis.

AIMS: To select Lactobacillus strains from laying hens for potential use as probiotic to control Salmonella Enteritidis infection. METHODS AND RESULTS: One hundred and eighty-six lactobacilli were isolated from the cloaca and vagina of laying hens, and identified at the species level by a polyphasic taxonomic approach. All isolates belonged to the Lactobacillus acidophilus, Lactobacillus reuteri or Lactobacillus salivarius phylogenetic groups, with the L. reuteri group being the most predominant group. Based on genetic diversity, about 50 representative strains were selected and tested for in vitro properties that could be predictive for probiotic activity in laying hens. Salmonella inhibition was shown to be species dependent, and correlated to some extent with the production of lactic acid. A selection of strains was evaluated in a S. Enteritidis challenge experiment. Two strains, L. reuteri R-17485 and Lactobacillus johnsonii R-17504 significantly decreased the colonization of chicks by S. Enteritidis in caeca, liver and spleen. CONCLUSIONS: Lactobacilli isolated from laying hens were observed to inhibit Salmonella growth in vitro, most probably through production of lactic acid, and to decrease in vivo the S. Enteritidis colonization of chicks. SIGNIFICANCE AND IMPACT OF THE STUDY: The data demonstrate that Lactobacillus isolates from laying hens may have probiotic potential in reducing S. Enteritidis infection.

Polyphasic identification of Bacillus and Brevibacillus strains from clinical, dairy and industrial specimens and proposal of Brevibacillus invocatus sp. nov..

Thirty-three clinical, dairy and industrial isolates of aerobic endospore-forming bacteria which were unreactive in routine identification tests were characterized genotypically by using amplified rDNA restriction analysis (ARDRA), 16S rDNA sequencing and DNA-DNA reassociation, and phenotypically by using fatty acid methyl ester (FAME) analysis, SDS-PAGE of whole-cell proteins, API Biotype 100 assimilation tests and 16 other routine phenotypic tests. Three isolates were identified as strains of Bacillus badius, 12 as Brevibacillus agri, including 3 strains associated with an outbreak of waterborne illness, 4 as Brevibacillus centrosporus and 2 as Brevibacillus parabrevis; 12 strains contaminating an antibiotic production plant were recognized as members of a new species, for which the name Brevibacillus invocatus is proposed, with the type strain LMG 18962T (= B2156T = CIP 106911T = NCIMB 13772T).

The presence of intragenically located REP-like elements in Bacillus sporothermodurans is sufficient for REP-PCR typing.

The technique of repetitive extragenic palindromic polymerase chain reaction (REP-PCR) enables the identification and discrimination of clonally related Bacillus sporothermodurans isolates from ultra-high temperature and sterilized milk. The aim of this study was to investigate the genetic basis for the generation of these highly informative REP-PCR patterns. The major 947-bp REP-PCR fragment of B. sporothermodurans was cloned, together with its 5' and 3' flanking sequences. Only partial homology with the REP consensus sequence was established at the borders of the REP-PCR fragment. Moreover, these border sequences were located within two distinct open reading frames, with great homology to the uvrA and uvrB genes of Escherichia coli. The presence of these REP-like elements in B. sporothermodurans was thus sufficient for high resolution REP-PCR typing of this Gram-positive organism. In some cases (and especially with Gram-positives), REP-PCR could thus be considered more as an arbitrary primed PCR, albeit at a somewhat higher annealing temperature and using conserved primers. The random priming effect at the less stringent annealing conditions of REP-PCR was also demonstrated for enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) on another Gram-positive organism, Listeria monocytogenes.

Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998.

A polyphasic study of strains originally received as Bacillus (now Virgibacillus) pantothenticus, along with strains representing species belonging to Bacillus, Halobacillus and Paenibacillus, was undertaken using amplified rDNA restriction analysis (ARDRA), fatty acid methyl ester (FAME) analysis, SDS-PAGE of whole-cell proteins and routine diagnostic characters comprising 61 biochemical tests in the API system and 15 observations of vegetative cell and sporangial morphology. It revealed the presence within Virgibacillus of an as yet undescribed new species, for which the name Virgibacillus proomii is proposed; V. proomii can be distinguished from V. pantothenticus and members of Bacillus sensu stricto, and from members of Paenibacillus and other aerobic endospore-forming bacteria, by routine phenotypic tests. The type strain of Virgibacillus proomii is LMG 12370T.

A polyphasic reassessment of the genus Paenibacillus, reclassification of Bacillus lautus (Nakamura 1984) as Paenibacillus lautus comb. nov. and of Bacillus peoriae (Montefusco et al. 1993) as Paenibacillus peoriae comb. nov., and emended descriptions of P. lautus and of P. peoriae.

Seventy-seven strains representing 10 species in the Paenibacillus polymyxa 16S rRNA group and 3 other species that exhibit phenetic relatedness to members of this group, Bacillus lautus, "Bacillus longisporus," and Bacillus peoriae, were characterized genotypically and phenotypically by performing an amplified ribosomal DNA restriction analysis, a randomly amplified polymorphic DNA analysis, a fatty acid methyl ester analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, pyrolysis mass spectrometry, and API and other routine phenotypic tests. These analyses revealed distinct clusters representing Paenibacillus alvei, Paenibacillus amylolyticus, Paenibacillus azotofixans, Paenibacillus durum, Paenibacillus larvae subsp. larvae, Paenibacillus larvae subsp. pulvifaciens, B. lautus, Paenibacillus macerans, Paenibacillus macquariensis, B. peoriae, P. polymyxa, and Paenibacillus validus, which confirmed the distinctness of these species, but appreciable within-species heterogeneity was observed in P. alvei, B. lautus, P. macerans, P. polymyxa, and P. validus. The type strain of Paenibacillus pabuli did not cluster with other strains of this species, and in several analyses a relationship between strains of P. pabuli and "B. longisporus" was observed. As the analyses showed that B. lautus and B. peoriae are closely related to the genus Paenibacillus, these species are reclassified as members of this genus.

Reclassification of Paenibacillus (formerly Bacillus) pulvifaciens (Nakamura 1984) Ash et al. 1994, a later subjective synonym of Paenibacillus (formerly Bacillus) larvae (White 1906) Ash et al. 1994, as a subspecies of P. larvae, with emended descriptions of P. larvae as P. larvae subsp. larvae and P. larvae subsp. pulvifaciens.

A polyphasic taxonomic study of four strains of Paenibacillus larvae and four strains of Paenibacillus pulvifaciens (including duplicates of both type strains) supported the reclassification of both former Bacillus species into one species, P. larvae. Our conclusions were based on morphological and Analytab Products (API) tests, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell proteins, gas chromatography of methylated fatty acids, pyrolysis mass spectrometry, DNA-DNA binding, and the following genomic fingerprinting methods: amplified ribosomal DNA restriction analysis, random amplified polymorphic DNA analysis, and AFLP analysis. The last method is a novel high-resolution DNA fingerprinting technique based on the selective amplification of restriction fragments. Despite more than 90% DNA relatedness between the strains studied, SDS-PAGE of whole-cell proteins, biochemical tests, and DNA fingerprinting (AFLP) distinguished between the P. larvae and P. pulvifaciens strains at the subspecies level. Taking this evidence along with differences in pathogenicity, we propose to reclassify the honeybee pathogens P. larvae and P. pulvifaciens as P. larvae subsp. larvae and P. larvae subsp. pulvifaciens. An emended description of the species and descriptions of the subspecies are given. The type strains are P. larvae subsp. larvae ATCC 9545 (LMG 9820) and P. larvae subsp. pulvifaciens NRRL B-3685 (LMG 6911 and ATCC 13537).

Paenibacillus (formerly Bacillus) gordonae (Pichinoty et al. 1986) Ash et al. 1994 is a later subjective synonym of Paenibacillus (formerly Bacillus) validus (Nakamura 1984) Ash et al. 1994: emended description of P. validus.

A polyphasic study in which we performed an amplified ribosomal DNA restriction analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, a gas chromatographic analysis of methylated fatty acids, pyrolysis mass spectrometry, a random amplified polymorphic DNA analysis, a phenotypic analysis, and an analysis of the levels of DNA binding of Paenibacillus gordonae and Paenibacillus validus strains (including both type strains) showed that these organisms form a homogeneous group and that the names P. gordonae and P. validus are therefore synonyms. P. validus has nomenclatural priority, and an emended description of this species is given; the type strain is strain LMG 11161 (= ATCC 43897).