Description of a new genus of the Pectobacteriaceae family isolated from water in coastal brackish wetlands of the French Camargue region, Prodigiosinella gen. nov., including the new species Prodigiosinella aquatilis sp. nov

The Pectobacteriaceae family comprises plant pathogens able to provoke diverse diseases, including plant maceration due to the production of pectinases disrupting the plant cell wall. To better understand their diversity, a survey of pectinolytic bacteria was performed in brackish lakes of the French region La Camargue near the Mediterranean Sea. The genome of six atypical isolates was sequenced; their size is around 4.8 to 5.0 Mb, including a plasmid of 59 to 61 kb; their G+C values range from 49.1 to 49.3 mol%. Phylogenetic analyses indicated that the novel strains form a new clade of Pectobacteriaceae that branches at the basis of the group encompassing the genera Lonsdalea, Musicola, and Dickeya. Based on phenotypic, genomic and phylogenetic characteristics, we propose the creation of a new genus with the name Prodigiosinella gen. nov. Both the phenotypic and phylogenetic analyses separated the strains into two distinct subgroups, G1 and G2. The type strain LS101T (CFBP 8826T = LMG 32072T) and strain CE70 (CFBP 9054 = LMG 32867) are representative G1 and G2 members, respectively. Three genomic methods were used to analyze DNA-DNA relatedness: digital DNA-DNA hybridization (isDDH), average nucleotide identity (ANI), and genome alignment fraction (AF). They revealed a close relationship between genomes of the two groups, supporting their appurtenance to a same species for which we propose the name Prodigiosinella aquatilis sp. nov. Four strains previously designated as Serratia sp. (ATCC 39006), Brenneria "ulupoensis" (K61) or Erwinia sp. (MK01 and MK09) belong to the new genus Prodigiosinella.

A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

Background

The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal.

Results

We analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study.

Conclusions

We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01952-0.

A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes

The cell cycle is a fundamental process that has been extensively studied in bacteria. However, many of its components and their interactions with machineries involved in other cellular processes are poorly understood. Furthermore, most knowledge relies on the study of a few models, but the real diversity of the cell division apparatus and its evolution are largely unknown. Here, we present a massive in-silico analysis of cell division and associated processes in around 1,000 genomes of the Firmicutes, a major bacterial phylum encompassing models (i.e. Bacillus subtilis, Streptococcus pneumoniae, and Staphylococcus aureus), as well as many important pathogens. We analyzed over 160 proteins by using an original approach combining phylogenetic reconciliation, phylogenetic profiles, and gene cluster survey. Our results reveal the presence of substantial differences among clades and pinpoints a number of evolutionary hotspots. In particular, the emergence of Bacilli coincides with an expansion of the gene repertoires involved in cell wall synthesis and remodeling. We also highlight major genomic rearrangements at the emergence of Streptococcaceae. We establish a functional network in Firmicutes that allows identifying new functional links inside one same process such as between FtsW (peptidoglycan polymerase) and a previously undescribed Penicilin-Binding Protein or between different processes, such as replication and cell wall synthesis. Finally, we identify new candidates involved in sporulation and cell wall synthesis. Our results provide a previously undescribed view on the diversity of the bacterial cell cycle, testable hypotheses for further experimental studies, and a methodological framework for the analysis of any other biological system.

Metapopulation ecology links antibiotic resistance, consumption, and patient transfers in a network of hospital wards

Antimicrobial resistance (AMR) is a global threat. A better understanding of how antibiotic use and between-ward patient transfers (or connectivity) impact population-level AMR in hospital networks can help optimize antibiotic stewardship and infection control strategies. Here, we used a metapopulation framework to explain variations in the incidence of infections caused by seven major bacterial species and their drug-resistant variants in a network of 357 hospital wards. We found that ward-level antibiotic consumption volume had a stronger influence on the incidence of the more resistant pathogens, while connectivity had the most influence on hospital-endemic species and carbapenem-resistant pathogens. Piperacillin-tazobactam consumption was the strongest predictor of the cumulative incidence of infections resistant to empirical sepsis therapy. Our data provide evidence that both antibiotic use and connectivity measurably influence hospital AMR. Finally, we provide a ranking of key antibiotics by their estimated population-level impact on AMR that might help inform antimicrobial stewardship strategies.

Dickeya poaceiphila sp. nov., a plant-pathogenic bacterium isolated from sugar cane (Saccharum officinarum)

The genus Dickeya is an important group of plant pathogens that currently comprises 10 recognized species. Although most Dickeya isolates originated from infected cultivated plants, they are also isolated from water. The genomic sequence of the Australian strain NCPPB 569^T clearly established its separation from the previously characterized Dickeya species. The average nucleotide identity and digital DNA-DNA hybridization values obtained by comparing strain NCPPB 569^T with strains of characterized Dickeya species were lower than 87 and 32 %, respectively, supporting the delineation of a new species. The name Dickeya poaceiphila sp. nov. is proposed for this taxon with the type strain NCPPB 569^T (=CFBP 8731^T). Two other strains isolated in Australia, CFBP 1537 and CFBP 2040, also belong to this species. Phenotypic and genomic comparisons enabled the identification of traits distinguishing D. poaceiphila isolates from strains of other Dickeya species.

Isotopic systematics point to wild origin of mummified birds in Ancient Egypt

Millions of mummified birds serving for religious purpose have been discovered from archeological sites along the Nile Valley of Egypt, in majority ibises. Whether these birds were industrially raised or massively hunted is a matter of heavy debate as it would have a significant impact on the economy related to their supply and cult, and if hunted it would have represented an ecological burden on the birds populations. Here we have measured and analysed the stable oxygen, carbon and radiogenic strontium isotope compositions as well as calcium and barium content of bones along with the stable carbon, nitrogen and sulfur isotope composition of feathers from 20 mummified ibises and birds of prey recovered from various archeological sites of Ancient Egypt. If these migratory birds were locally bred, their stable oxygen, radiogenic strontium and stable sulfur isotopic compositions would be similar to that of coexisting Egyptians, and their stable carbon, nitrogen and oxygen isotope variance would be close, or lower than that of Egyptians. On one hand, isotopic values show that ibises ingested food from the Nile valley but with a higher isotopic scattering than observed for the diet of ancient Egyptians. On the other hand, birds of prey have exotic isotopic values compatible with their migratory behaviour. We therefore propose that most mummified ibises and all the birds of prey analysed here were wild animals hunted for religious practice.

A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

Amplicon sequencing of the 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations, with the most significant being the inability to resolve mixed amplicons when closely related species are coamplified from a mixed culture. This often leads to either increased turnaround time or absence of usable sequence data. Short-read next-generation sequencing (NGS) technologies could solve the mixed amplicon issue but would lack both cost efficiency at low throughput and fast turnaround times. Nanopore sequencing developed by Oxford Nanopore Technologies (ONT) could solve those issues by enabling a flexible number of samples per run and an adjustable sequencing time. Here, we report on the development of a standardized laboratory workflow combined with a fully automated analysis pipeline LORCAN (long read consensus analysis), which together provide a sample-to-report solution for amplicon sequencing and taxonomic identification of the resulting consensus sequences. Validation of the approach was conducted on a panel of reference strains and on clinical samples consisting of single or mixed rRNA amplicons associated with various bacterial genera by direct comparison to the corresponding Sanger sequences. Additionally, simulated read and amplicon mixtures were used to assess LORCAN's behavior when dealing with samples with known cross-contamination levels. We demonstrate that by combining ONT amplicon sequencing results with LORCAN, the accuracy of Sanger sequencing can be closely matched (>99.6% sequence identity) and that mixed samples can be resolved at the single-base resolution level. The presented approach has the potential to significantly improve the flexibility, reliability, and availability of amplicon sequencing in diagnostic settings.

Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon

The taxonomic assignment of uncultured prokaryotes to known taxa is a major challenge in microbial systematics. This relies usually on the phylogenetic analysis of the ribosomal small subunit RNA or a few housekeeping genes. Recent works have disclosed ribosomal proteins as valuable markers for systematics and, due to the boom in complete genome sequencing, their use has become widespread. Yet, in the case of uncultured strains, for which complete genome sequences cannot be easily obtained, sequencing many markers is complicated and time consuming. Taking the advantage of the organization of ribosomal protein coding genes in large gene clusters, we amplified a 32 kb conserved region encompassing the spectinomycin (spc) operon using long range PCR from isolated and from uncultured nodular endophytic Frankia strains. The phylogenetic analysis of the 27 ribosomal protein genes contained in this region provided a robust phylogenetic tree consistent with phylogenies based on larger set of markers, indicating that this subset of ribosomal proteins contains enough phylogenetic signal to address systematic issues. This work shows that using long range PCR could break down the barrier preventing the use of ribosomal proteins as phylogenetic markers when complete genome sequences cannot be easily obtained.

The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Dickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep-branching species among Dickeya genus, its precise phylogenetic position remained elusive. Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquatica strain 174/2 for acidic fruits such as tomato and cucumber and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes, we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothesize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflect adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.

Record of Nile seasonality in Nubian neonates

The oxygen isotope compositions of bones (n = 11) and teeth (n = 20) from 12 Sudanese individuals buried on Sai Island (Nubia) were analysed to investigate the registration of the evolution of the Nile environment from 3700 to 500 years BP and the potential effects of ontogeny on the oxygen isotope ratios. The isotopic compositions were converted into the composition of drinking water, ultimately originating from the Nile. δ¹⁸O values decrease during ontogeny; this is mainly related to breastfeeding and physiology. Those of neonates present very large variations. Neonates have a very high bone turnover and are thus able to record seasonal δ¹⁸O variations of the Nile waters. These variations followed a pattern very similar to the present one. Nile δ¹⁸O values increased from 1.4 to 4.4 ‰ (Vienna Standard Mean Ocean Water) from the Classic Kerma (∼3500 BP) through the Christian period (∼1000 BP), traducing a progressive drying of Northeast Africa.

Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

The transmission dynamics of tuberculosis involves complex interactions of socio-economic and, possibly, microbiological factors. We describe an analytical framework to infer factors of epidemic success based on the joint analysis of epidemiological, clinical and pathogen genetic data. We derive isolate-specific, genetic distance-based estimates of epidemic success, and we represent success-related time-dependent concepts, namely epidemicity and endemicity, by restricting analysis to specific time scales. The method is applied to analyze a surveillance-based cohort of 1,641 tuberculosis patients with minisatellite-based isolate genotypes. Known predictors of isolate endemicity (older age, native status) and epidemicity (younger age, sputum smear positivity) were identified with high confidence (P < 0.001). Long-term epidemic success also correlated with the ability of Euro-American and Beijing MTBC lineages to cause active pulmonary infection, independent of patient age and country of origin. Our results demonstrate how important insights into the transmission dynamics of tuberculosis can be gained from active surveillance data.

RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics

Ribosomal proteins (r-proteins) are increasingly used as an alternative to ribosomal rRNA for prokaryotic systematics. However, their routine use is difficult because r-proteins are often not or wrongly annotated in complete genome sequences, and there is currently no dedicated exhaustive database of r-proteins. RiboDB aims at fulfilling this gap. This weekly updated comprehensive database allows the fast and easy retrieval of r-protein sequences from publicly available complete prokaryotic genome sequences. The current version of RiboDB contains 90 r-proteins from 3,750 prokaryotic complete genomes encompassing 38 phyla/major classes and 1,759 different species. RiboDB is accessible at http://ribodb.univ-lyon1.fr and through ACNUC interfaces.

leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences

BACKGROUND

Estimating the phylogenetic position of bacterial and archaeal organisms by genetic sequence comparisons is considered as the gold-standard in taxonomy. This is also a way to identify the species of origin of the sequence. The quality of the reference database used in such analyses is crucial: the database must reflect the up-to-date bacterial nomenclature and accurately indicate the species of origin of its sequences.

DESCRIPTION

leBIBI(QBPP) is a web tool taking as input a series of nucleotide sequences belonging to one of a set of reference markers (e.g., SSU rRNA, rpoB, groEL2) and automatically retrieving closely related sequences, aligning them, and performing phylogenetic reconstruction using an approximate maximum likelihood approach. The system returns a set of quality parameters and, if possible, a suggested taxonomic assigment for the input sequences. The reference databases are extracted from GenBank and present four degrees of stringency, from the "superstringent" degree (one type strain per species) to the loosely parsed degree ("lax" database). A set of one hundred to more than a thousand sequences may be analyzed at a time. The speed of the process has been optimized through careful hardware selection and database design.

CONCLUSION

leBIBI(QBPP) is a powerful tool helping biologists to position bacterial or archaeal sequence commonly used markers in a phylogeny. It is a diagnostic tool for clinical, industrial and environmental microbiology laboratory, as well as an exploratory tool for more specialized laboratories. Its main advantages, relatively to comparable systems are: i) the use of a broad set of databases covering diverse markers with various degrees of stringency; ii) the use of an approximate Maximum Likelihood approach for phylogenetic reconstruction; iii) a speed compatible with on-line usage; and iv) providing fully documented results to help the user in decision making.

Mycobacterium species related to M. leprae and M. lepromatosis from cows with bovine nodular thelitis

Bovine nodular thelitis is a granulomatous dermatitis associated with infection with acid-fast bacteria. To identify the mycobacterium responsible for this infection, we conducted phylogenetic investigations based on partial sequencing of 6 genes. These bacteria were identified as an undescribed Mycobacterium species that was phylogenetically related to M. leprae and M. lepromatosis.

Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS

On the ISS, as on Earth, water is an essential element for life and its quality control on a regular basis allows to ensure the health of the crew and the integrity of equipment. Currently, microbial water analysis onboard ISS still relies on the traditional culture-based microbiology methods. Molecular methods based on the amplification of nucleic acids for microbiological analysis of water quality show enormous potential and are considered as the best alternative to culture-based methods. For this reason, the Midass, a fully integrated and automated prototype was designed conjointly by ESA and bioMérieux for a rapid monitoring of the microbiological quality of air. The prototype allows air sampling, sample processing and the amplification/detection of nucleic acids. We describe herein the proof of principle of an analytical approach based on molecular biology that could fulfill the ESA's need for a rapid monitoring of the microbiological quality of recycled water onboard ISS. Both concentration and recovery of microorganisms are the main critical steps when the microfiltration technology is used for water analysis. Among filters recommended standards for monitoring the microbiological quality of the water, the polycarbonate filter was fully in line with the requirements of the ISO 7704-1985 standard in terms of efficacy of capture and recovery of bacteria. Moreover, this filter does not retain nucleic acids on the surface and has no inhibitory effect on their downstream processing steps such as purification and amplification/detection. Although the Midass system was designed for the treatment of air samples, the first results on the integration of PC filters were encouraging. Nevertheless, system modifications are needed to better adapt the Midass system for the monitoring of the microbiological water quality.

Monod's bacterial growth model revisited

An attempt to justify Monod's bacterial growth model is presented. The justification is based on a mechanistic approach to growth which leads to a differential equation with delay and then to Monod's model. An unexpected increase of parameter K(s) with μm is predicted by the theory. A survey of literature shows that this effect is present in a large majority of published data.

Nontuberculous Mycobacteria: An Underestimated Cause of Bioprosthetic Valve Infective Endocarditis

From 2010 to 2013, 5 cases of nontuberculous mycobacteria infective endocarditis (IE), exclusively from bioprosthesis, were diagnosed in three hospitals out of 370 blood culture-negative-suspected IE. The porcine origin of this underestimated etiology is questioned.

Background. Atypical mycobacteria, or nontuberculous mycobacteria (NTM), have been barely reported as infective endocarditis (IE) agents.

Methods. From January 2010 to December 2013, cardiac valve samples sent to our laboratory as cases of blood culture-negative suspected IE were analyzed by 16S rDNA polymerase chain reaction (PCR). When positive for NTM, hsp PCR allowed species identification. Demographic, clinical, echocardiographic, histopathological, and Ziehl-Neelsen staining data were then collected.

Results. Over the study period, 6 of 370 cardiac valves (belonging to 5 patients in 3 hospitals) were positive for Mycobacterium chelonae (n = 5) and Mycobacterium lentiflavum (n = 1) exclusively on bioprosthetic material. The 5 patients presented to the hospital for heart failure without fever 7.1–18.9 months (median 13.1 months) after biological prosthetic valve implantation. Echocardiography revealed paravalvular regurgitation due to prosthesis dehiscence in all patients. Histopathological examination of the explanted material revealed inflammatory infiltrates in all specimens, 3 of which were associated with giant cells. Gram staining and conventional cultures remained negative, whereas Ziehl-Neelsen staining showed acid-fast bacilli in all patients. Allergic etiology was ruled out by antiporcine immunoglobulin E dosages. These 5 cases occurred exclusively on porcine bioprosthetic material, revealing a statistically significant association between bioprosthetic valves and NTM IE (P < .001).

Conclusions. The body of evidence confirmed the diagnosis of prosthetic IE. The statistically significant association between bioprosthetic valves and NTM IE encourages systematic Ziehl-Neelsen staining of explanted bioprosthetic valves in case of early bioprosthesis dysfunction, even without an obvious sign of IE. In addition, we strongly question the cardiac bioprosthesis conditioning process after animal sacrifice.

MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis

Background

Tuberculosis is an infectious bacterial disease caused by Mycobacterium tuberculosis. It remains a major health threat, killing over one million people every year worldwide. An early antibiotic therapy is the basis of the treatment, and the emergence and spread of multidrug and extensively drug-resistant mutant strains raise significant challenges. As these bacteria grow very slowly, drug resistance mutations are currently detected using molecular biology techniques. Resistance mutations are identified by sequencing the resistance-linked genes followed by a comparison with the literature data. The only online database is the TB Drug Resistance Mutation database (TBDReaM database); however, it requires mutation detection before use, and its interrogation is complex due to its loose syntax and grammar.

Description

The MUBII-TB-DB database is a simple, highly structured text-based database that contains a set of Mycobacterium tuberculosis mutations (DNA and proteins) occurring at seven loci: rpoB, pncA, katG; mabA(fabG1)-inhA, gyrA, gyrB, and rrs. Resistance mutation data were extracted after the systematic review of MEDLINE referenced publications before March 2013. MUBII analyzes the query sequence obtained by PCR-sequencing using two parallel strategies: i) a BLAST search against a set of previously reconstructed mutated sequences and ii) the alignment of the query sequences (DNA and its protein translation) with the wild-type sequences. The post-treatment includes the extraction of the aligned sequences together with their descriptors (position and nature of mutations). The whole procedure is performed using the internet. The results are graphs (alignments) and text (description of the mutation, therapeutic significance). The system is quick and easy to use, even for technicians without bioinformatics training.

Conclusion

MUBII-TB-DB is a structured database of the mutations occurring at seven loci of major therapeutic value in tuberculosis management. Moreover, the system provides interpretation of the mutations in biological and therapeutic terms and can evolve by the addition of newly described mutations. Its goal is to provide easy and comprehensive access through a client–server model over the Web to an up-to-date database of mutations that lead to the resistance of M. tuberculosis to antibiotics.

Mycobacterium bourgelatii sp. nov., a rapidly growing, non-chromogenic species isolated from the lymph nodes of cattle

Three independent strains of a rapidly growing, non-chromogenic member of the genus Mycobacterium were isolated from lymph nodes of French cattle. Identification of the isolates was carried out using a polyphasic approach. The nearly complete SSU rRNA gene sequences (>1200 bp) of the strains MLB-A23, MLB-A30 and MLB-A84(T) were identical. A phylogenetic analysis of these unique SSU rRNA gene sequences showed that these strains were most closely related to Mycobacterium intermedium. Further phylogenetic analysis based on concatenated sequences (2854 bp) of four housekeeping genes (hsp65, rpoB, sodA and tuf), the transfer-messenger RNA (tmRNA) and SSU rRNA genes indicated that these three strains represented a distinct species that shares a common ancestor with M. intermedium. Phylogenetic and phenotypic data strongly indicate that the strains MLB-A23, MLB-A30 and MLB-A84(T) belong to a novel mycobacterial species for which the name Mycobacterium bourgelatii sp. nov. is proposed. The type strain is MLB-A84(T) ( = CIP 110557(T) = DSM 45746(T)).

Diminution of 2,3,5-triphenyltetrazolium chloride toxicity on Listeria monocytogenes growth by iron source addition to the culture medium

Tetrazolium salts (TTZ) such as 2,3,5-triphenyltetrazolium chloride (TTC) are readily reduced by bacterial populations of various genus. The reduced form of these redox indicators is conspicuously colored allowing a quick and easy detection of growth. The studies are mainly confined to Gram negative bacteria because of an important toxic effect of tetrazolium salts on Gram positive bacteria. Indeed, we observed an important impact of different tetrazolium salts on Listeria monocytogenes growth, curiously limited to an increase in the duration of the lag phase. In this study, we demonstrate that increasing the iron concentration in a medium containing TTC leads to a significant decrease of the lag phase. L. monocytogenes growth was kinetically measured and growth parameters were estimated using the Baranyi model. While lag phase diminution was found to be iron concentration dependent, growth rate was not affected. Addition of iron enables growth of some strains totally inhibited by a 0.4 g/l of TTC and for the other a significant reduction of the latency is observed. The nature of the mechanism resulting in a decrease of the observed lag phase remains unclear. Then, the use of iron supplementation may be proposed to overcome the inhibitory effect of TTC on L. monocytogenes.

Identification of Mycobacterium using the EF-Tu encoding (tuf) gene and the tmRNA encoding (ssrA) gene

The partial nucleotide sequences encoding the elongation factor Tu (tuf gene) (652 bp) and transfer-mRNA (tmRNA or ssrA gene) (340 bp) were determined to assess the suitability of these two genes as phylogenetic markers for the classification of mycobacteria, and thus as alternative target molecules for identifying mycobacteria. A total of 125 reference strains of the genus Mycobacterium and 74 clinical isolates were amplified by PCR and sequenced. Phylogenies of the two genes constructed by the neighbour-joining method were created and compared to a concatenated tree of 16S rDNA, hsp65, sodA and rpoB genes. The phylogenetic trees revealed the overall natural relationships among Mycobacterium species. The tmRNA phylogeny was similar to that of 16S rDNA, with low resolving power. The tuf gene provided better resolution of each mycobacterial species, with a phylogeny close to that of hsp65. However, none of these methods differentiated between the members of the Mycobacterium tuberculosis complex or the subspecies of the Mycobacterium avium complex. The correct identification of clinical isolates confirms the interest of these genes, especially tuf. It is suggested from these findings that tmRNA might be useful as another housekeeping gene in a polyphyletic approach to Mycobacterium species, but not as a first-line marker of species. tuf gene analysis suggests that this gene could be used effectively for phylogenetic analysis and to identify mycobacteria.

Rapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene

Real-time polymerase chain reaction and sequencing were used to characterize a 506-bp-long DNA fragment internal to the gyrB gene (gyrBint). The sequences obtained from 32 Enterobacteriaceae-type strains and those available in the Genbank nucleotide sequence database (n = 24) were used as a database to identify 240 clinical enterobacteria isolates. Sequence analysis of the gyrBint fragment of 240 strains showed that gyrBint constitutes a discriminative target sequence to differentiate between Enterobacteriaceae species. Comparison of these identifications with those obtained by phenotypic methods (Vitek 1 system and/or Rapid ID 32E; bioMérieux, Marcy l'Etoile, France) revealed discrepancies essentially with genera Citrobacter and Enterobacter. Most of the strains identified as Enterobacter cloacae by phenotypic methods were identified as Enterobacter hormaechei strains by gyrBint sequencing. The direct sequencing of gyrBint would be useful as a complementary tool in the identification of clinical Enterobacteriaceae isolates.

Use of PCR-restriction enzyme pattern analysis and sequencing database for hsp65 gene-based identification of Nocardia species

Nocardia identification required laborious and time-consuming phenotypic and chemotaxonomic methods until molecular methods were developed in the mid-1990s. Here we reassessed the capacity of PCR-restriction enzyme pattern analysis (PRA) of the hsp65 gene to differentiate Nocardia species, including 36 new species. Our results confirm that hsp65 PRA must no longer be used for Nocardia species identification, as many species have the same restriction pattern. We then compared sequencing-based strategies using an hsp65 database and a 16S rRNA database and found that the hsp65 region contained sufficient polymorphisms for comprehensive Nocardia species identification.

A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model

Advances in DNA sequencing and the increasing number of sequences available in databases have greatly enhanced the bacterial identification process. Several species within the genusMycobacteriumcause serious human and animal diseases. In order to assess their relative positions in the evolutionary process, four gene fragments, from the 16S rRNA (564 bp),hsp65(420 bp),rpoB(396 bp) andsod(408 bp) genes, were sequenced from 97 strains, including all available type strains of the genusMycobacterium. The results demonstrate that, in this case, the concatenation of different genes allows significant increases in the power of discrimination and the robustness of the phylogenetic tree. The sequential and/or combined use of sequences of several genes makes it possible to refine the phylogenetic approach and provides a molecular basis for accurate species identification.

How does susceptibility prevalence impact on the performance of disk diffusion susceptibility testing?

Antimicrobial disk diffusion susceptibility testing, devoted in a clinical context to predicting whether an antibiotic regimen will be effective, should be evaluated through predictive values. This approach implies that the susceptibility prevalence (frequency of susceptible, intermediate, and resistant isolates) affects the predictive value of a result. We quantified the influence of the susceptibility prevalence variation on the disk diffusion method performance through a modeling approach. Simulations based on a resampling procedure from two distinct minimum inhibitory concentration/diameter data sets were performed. Experimental variability on minimum inhibitory concentration and diameters was taken into account in the simulations. Results show that the susceptibility prevalence impact depends on the antibiotic and may be significant when prevalence variation is high enough. Consequences of these results on zone diameter breakpoint determination policy are discussed. This implies that the following should be done: (i) consider more rigorously the susceptibility prevalence in studies dealing with zone diameter breakpoint determination and performance evaluation, (ii) re-evaluate disk diffusion breakpoint consistency when the weight of prevalence variation is noteworthy, (iii) estimate consequences of a breakpoint international consensus on prediction quality and appropriate patient management.

BIBI, a bioinformatics bacterial identification tool

BIBI was designed to automate DNA sequence analysis for bacterial identification in the clinical field. BIBI relies on the use of BLAST and CLUSTAL W programs applied to different subsets of sequences extracted from GenBank. These sequences are filtered and stored in a new database, which is adapted to bacterial identification.

Modeling the lag time of Listeria monocytogenes from viable count enumeration and optical density data

The following two factors significantly influence estimates of the maximum specific growth rate ( micro (max)) and the lag-phase duration (lambda): (i) the technique used to monitor bacterial growth and (ii) the model fitted to estimate parameters. In this study, nine strains of Listeria monocytogenes were monitored simultaneously by optical density (OD) analysis and by viable count enumeration (VCE) analysis. Four usual growth models were fitted to our data, and estimates of growth parameters were compared from one model to another and from one monitoring technique to another. Our results show that growth parameter estimates depended on the model used to fit data, whereas there were no systematic variations in the estimates of micro (max) and lambda when the estimates were based on OD data instead of VCE data. By studying the evolution of OD and VCE simultaneously, we found that while log OD/VCE remained constant for some of our experiments, a visible linear increase occurred during the lag phase for other experiments. We developed a global model that fits both OD and VCE data. This model enabled us to detect for some of our strains an increase in OD during the lag phase. If not taken into account, this phenomenon may lead to an underestimate of lambda.

What is the relevance of obtaining multiple blood samples for culture? A comprehensive model to optimize the strategy for diagnosing bacteremia

Through a heuristic and probabilistic approach, we evaluated blood culture operating characteristics (sensitivity, specificity, and predictive values) as a function of several pretest parameters, together with their variability. On the basis of a meta-analysis of quantitative data from the literature, a model was developed and an estimation of the operating characteristics through numerical simulations (Monte Carlo method) was performed. The model evaluates the influence of ordering and drawing parameters on the ability of blood culture to distinguish bacteremic from nonbacteremic patients, regardless of the causative species. By considering the total blood volume to be cultured (six 5-10-mL bottles), results were found to confirm the current guidelines. On the basis of this hypothesis, the results, together with an analysis of the literature, failed to show any benefit of a strategy that involves obtaining multiple samples. The best strategy when performing blood culture is to obtain blood for 6 bottles (for a total volume of 35-42 mL), preferably at the same time.

Modelling the competitive growth of Listeria monocytogenes and Listeria innocua in enrichment broths

The overgrowth of Listeria innocua in enrichment broths designed for the isolation of Listeria monocytogenes is believed to result from two factors: a selective growth advantage of L. innocua, and/or an inhibitory interspecies interaction. The generation times of 13 isolates of L. innocua and L. monocytogenes were determined in Brain Heart Infusion (BHI) and a variety of enrichment media. No significant differences were found in growth characteristics between either species in the various media, suggesting that the growth advantage of L. innocua in enrichment media was not as significant as previously described. Kinetic analysis of mixed cultures of L. monocytogenes and isolates of L. innocua producing a variety of inhibitory activities demonstrated the possibility of an inhibitory interaction between these two species resulting in the overgrowth of the enrichment culture with L. innocua. Modelling the evolution of the ratio between two populations in an enrichment process was used to analyze the impact of a selective growth advantage in L. innocua in an enrichment process for growth of L. monocytogenes. These findings support the widely held view that an overgrowth of L. innocua in the enrichment process can result from both a selective growth advantage as well as the production of inhibitory compounds. From a practical perspective, these interactions can result in an increase in false negatives.

A mathematical model describing the thermal virus inactivation

A new mathematical model is proposed to describe the inactivation of viruses at different temperatures. This model takes into account the exponential decrease of the viral titer with time, the inactivation rate being an exponential function of the temperature. A one-step non-linear regression was used to fit oral poliovirus vaccine (OPV) experimental data. In one of the applications of the model, we illustrate the use of our model to compare the accelerated degradation test of OPV new formulations to standard OPV. Such a model is both simple and convenient to use. It should be a useful tool in optimizing formulations for live viral vaccines.

Fitness and competitive growth advantage of new gentamicin-susceptible MRSA clones spreading in French hospitals

Since 1991, new epidemic methicillin-resistant Staphylococcus aureus (MRSA) strains characterized by the unexpected reappearance of heterogeneous phenotypic expression of resistance to methicillin and by susceptibility to gentamicin and various other antibiotics (GS-MRSA) have been reported in France. GS-MRSA strains have progressively replaced MRSA clones expressing homogeneous resistance to methicillin and resistance to gentamicin (GR-MRSA). In this study, we investigated the physiological characteristics of these new clones. In particular, we evaluated and compared the maximal growth rate and the deduced generation times (related to fitness of strains) of the major French epidemic MRSA clones. The population studied consisted of 79 isolates including (i) GR-MRSA that comprised six different types on the basis of PFGE; (ii) GS-MRSA the majority of which clustered into two PFGE types, A1 (usually resistant to erythromycin) and B (usually susceptible to erythromycin); (iii) methicillin-susceptible S. aureus (MSSA). GS-MRSA-A1 and MSSA strains were shown to have a significant fitness benefit (about 20%) with shorter generation times (theta = 23.7 +/- 0.1 and 22.9 +/- 0.05 min, respectively) than GR-MRSA and GS-MRSA-B strains (theta = 30.3 +/- 0.2 and 32.5 +/- 0.5 min, respectively). These data suggest that a link exists between genetic patterns, resistance profiles and physiological properties. In vitro competitive experiments indicated that GS-MRSA- A1 strains were able to rapidly outgrow GR-MRSA strains. The growth advantage observed should be taken into account in understanding the spread of some new clones of MRSA.

Characterization of unexpected growth of Escherichia coli O157:H7 by modeling

Modeling of batch kinetics in minimal synthetic medium was used to characterize Escherichia coli O157:H7 growth, which appeared to be different from the exponential growth expected in minimal synthetic medium and observed for E. coli K-12. The turbidimetric kinetics of 14 of the 15 O157:H7 strains tested (93%) were nonexponential, whereas 25 of the 36 other E. coli strains tested (70%) exhibited exponential kinetics. Moreover, the anomaly was almost corrected when the minimal medium was supplemented with methionine. These observations were confirmed with two reference strains by using plate count monitoring. In mixed cultures, E. coli K-12 had a positive effect on E. coli O157:H7 and corrected its growth anomaly. This demonstrated that commensalism occurred, as the growth curve for E. coli K-12 was not affected. The interaction could be explained by an exchange of methionine, as the effect of E. coli K-12 on E. coli O157:H7 appeared to be similar to the effect of methionine.

A model describing the relationship between regrowth lag time and mild temperature increase for Listeria monocytogenes

In order to comply with the consumer demand for ready-to-eat and look 'fresh' products, mild heat treatment will be used more and more in the agrofood industry. Nonetheless there is no tool to define the most appropriate mild heat treatment. In order to build this tool, it is necessary to study and describe the response of a bacterial population to a mild increase in temperature, from the dynamic point of view. The response to a mild increase in temperature, defined by stress duration and temperature, consisted in a mortality phase followed by the lag time of the survivors and their exponential growth. The effect of the mild increase in temperature on the mortality phase was described in a previous paper (Bréand et al., Int. J. Food Microbiol., in press). The effect of the stress duration on the lag was presented in a previous paper (Bréand et al., Int. J. Food Microbiol. 38 (1997) 157-167). In particular, the biphasic relationship between the lag and the stress duration was observed and modelled with a four parameter nonlinear model: the primary model (Bréand et al., Int. J. Food Microbiol. 38 (1997) 157-167). The study presented in this paper deals with the effect of the stress temperature on the biphasic relationship between the lag time and the stress duration. The secondary models describing the effect of the stress temperature on this biphasic relationship, were empirically built from our experimental data concerning Listeria monocytogenes. This work pointed out that the higher the stress temperature, the narrower the range of stress duration for which the lag time increased. Since the primary and the secondary models of the lag time were available, the global model describing the effect of the mild increase duration and temperature directly on the lag was fitted. This model allowed an improvement of the parameter estimator precision. The potential contribution in mild heat treatment optimization of this global model and the one built for the mortality phase (Bréand et al., Int. J. Food Microbiol., in press) is discussed.

Model of the influence of time and mild temperature on Listeria monocytogenes nonlinear survival curves

Heat treatment has long been regarded as one of the most widely used and most effective means of destroying pathogens in food. Up to now the linear relationship between the death rate and the temperature has been used when choosing the best heat treatment to apply. However, the information given by this linear relationship is no longer sufficient when nonlinear survival curves are observed. Consequently, the agri-food industry needs a tool to choose the best mild heat treatment to apply in the case of nonlinear survival curves. This study deals with the temperature-induced death of Listeria monocytogenes CIP 7831 in the stationary phase of growth. Eleven temperatures were tested. With the proposed primary and secondary models good fits of our data were obtained. A model describing both the effect of the duration of treatment and the temperature on the logarithm of the number of survivors was then built. A clear increase in the precision of the estimation of the parameters was obtained with this model. Moreover, with this model a new graphical strategy to choose a mild heat increase regarding a maximal survivor number has been proposed.

Reappraisal of the effect of temperature on the growth kinetics of Aeromonas salmonicida

The effect of temperature (1-34 degrees C) on the maximum specific growth rate of Aeromonas salmonicida could not be described by the classical growth models; for some strains, two optimal temperatures at 23 degrees C and 30 degrees C were observed, as well as an unexpected increase in the pseudolag time above 27 degrees C. This could be explained by the presence of two subsets, notably S-layer+ and S-layer- sub-populations. The A- cells had higher growth parameters (Topt and mu opt) than the A+ cells and were selected by subcultures above 30 degrees C. Yet the relative proportion of A+ cells did not explain all the variation of mu max versus temperature, and the growth kinetics of an Aer. salmonicida isolate remained unpredictable.

A model describing the relationship between lag time and mild temperature increase duration

When a bacterial population undergoes an unfavourable increase in temperature for a given duration, called stress duration, a death phase followed by a lag and a growth phase are observed. The lag phase is actually of great interest in regard to foodstuff safety in choosing a suitable protocol for the detection of microorganisms which have undergone a mild heat treatment. The extension of lag time with the severity of the increase in temperature has been highlighted by previous papers. Our experimental results concerning Listeria monocytogenes and Escherichia coli revealed that a two phase relationship between lag time and stress duration is observed for a specific increase in temperature. The first phase consists of an increase in lag time up to a peak; the second one consists of a decrease from this peak to a steady threshold. The mathematical model presented, describing the relationship between lag time and stress duration was empirically built from our experimental data concerning L. monocytogenes and E. coli. The fit evaluation carried out led us to consider this model as a good description of the relationship studied. The potential contribution of our model in heat treatment optimization is discussed.

Homogeneous two-site immunometric assay kinetics as a theoretical tool for data analysis

The easily accessible kinetics of a new homogeneous two-site fluorometric immunoassay for prolactin was studied, in order to determine its usefulness for assay data reduction and optimization. The combined use of a simple descriptive model fitted to experimental data and a mechanistic model to simulate the kinetics revealed that (i) the kinetics curve presented an early inflexion point. Its time of occurrence was constant as long as the antigen concentration was below the smallest antibody concentration and decreased to zero for higher concentrations. It may therefore be used as an indicator of hooked samples. (ii) The kinetics steepest slope was correlated with antigen concentration. Its use as a dose-response curve variable would allow higher concentrations to be assayed than with the classical end-point dose-response curve. The results suggest that control and exploitation of kinetic parameters could help to improve the rapidity, analytical range, and reliability of homogeneous two-site immunometric assays.

Simple relationship between acid dissociation constant and minimal pH for microbial growth in laboratory medium

A simple relationship was observed in growth medium, between the dissociation constant (via the pKa) of the acid used to control pH and the minimum pH at which Salmonellae and Escherichia coli initiate growth. From this new relationship, a simple method was proposed to predict the minimum growth pH for a given strain and different acid types. This method, illustrated on Listeria monocytogenes, would merely require the knowledge of two minimum pH values, one for a strong acid (e.g. hydrochloric acid) and one for a weak acid (e.g. acetic or propionic acid). From these two values, it seems possible to estimate for a given growth medium, the minimum pH value for any other acid within the defined pKa range.

A descriptive model for the kinetics of a homogeneous fluorometric immunoassay

A descriptive mathematical model was chosen to fit the antigen-antibody association kinetics of a new homogeneous immunometric assay for prolactin, involving time-resolved fluorescence detection (TRACE technology, Time Resolved Amplified Cryptate Emission). We paid special attention to the methodology and criteria applied, to yield a convenient and statistically valid model, designed to allow potential exploitation of kinetic information in the data processing of the assay. We compared specific parameterizations of an hyperbolic model, the Gompertz, and the monomolecular models on the basis of morphological considerations, a statistical analysis of fit, and an assessment of the parameters estimation quality, over a wide range of antigen concentrations. The monomolecular model gave the best fit, and the most precise and stable estimation of its parameters. The study of parameter properties confirmed this choice.

Differential growth of Listeria monocytogenes at 4 and 8°C: Consequences for the Shelf Life of Chilled Products

Growth rates and lag times of Listeria monocytogenes at 4 and 8°C were compared in dairy products (milk, cream, and cheese), minced beef, and smoked salmon. Results showed that an increase in incubation temperature from 4 to 8°C leads to a significant decrease in time required to reach a given bacterial population density. The decreases were about 50% on cheese surfaces, 60 to 65% in milk and cream, and 75 to 80% in minced beef and smoked salmon. Consequences on the shelf life of chilled products are discussed on the basis of a simple and general linear relationship between the relative decrease in shelf life and generation time. This relationship was experimentally highlighted and theoretically demonstrated.

Application of a modified disc diffusion technique to antimicrobial susceptibility testing of Vibrio anguillarum and Aeromonas salmonicida clinical isolates

Two techniques for antimicrobial susceptibility testing of Vibrio anguillarum and Aeromonas salmonicida strains were compared. The first method was the reference test that determines Minimal Inhibitory Concentrations (MIC); the second was a modified diffusion test that measures the Inhibitory Concentrations in Diffusion (ICD) by carrying out the diffusion test with five discs of differing contents. ICD measurement was not applicable for the susceptibility testing of oxytetracycline and sulfadimethoxine. On the other hand, a good correlation between the MICs and the ICDs was observed for oxolinic acid, sarafloxacin, chloramphenicol and trimethoprim. Moreover, the ICD values were close to those obtained for the MIC values. A. salmonicida resistant strains were detected by ICD determination. Thus, ICD could be used instead of MIC for oxolinic acid, sarafloxacin, trimethoprim and chloramphenicol susceptibility testings. The ICD technique is easy to carry out and is not dependent on the growth characteristics of bacteria.

An economic approach to the MIC

The determination of the Inhibitory Concentration in Diffusion (ICD) is proposed as an alternative to the agar dilution Minimal Inhibitory Concentration (MIC) that is time-consuming and cumbersome for routine use. Based on the technique of the disk diffusion test, it consists in calculating a continuous variable, the ICD, corresponding to the antibiotic concentration in the agar at the edge of the inhibition zone. Six antibiotics were tested (ampicillin, cefotaxime, erythromycin, gentamicin, nalidixic acid and rifampicin) each against 17 to 51 strains of enterobacteria, Staphylococcus aureus and Enterococcus spp. and six other antibiotics (cefsulodin, ceftazidime, imipenem, piperacillin, ticarcillin and tobramycin), against 13 to 25 strains of Pseudomonas aeruginosa. A total of 284 antibiotic-strain combinations were tested. Three different antibiotic charges were obtained for each antibiotic by cutting commercial disks in two and four equal pieces. The ICD was calculated for each strain from the size of inhibition zones around a full disk, a half and a quarter of a disk. Concurrently, the MIC was performed, using a conventional agar dilution method. There was a good correlation between the two methods and reproducibility for the ICD proved to be correct. This reliable technique is very efficient both in terms of laboratory time and cost of materials and could be proposed for widespread use in clinical laboratories.

The particular behaviour of Listeria monocytogenes under sub-optimal conditions

Listeria monocytogenes is a ubiquitous pathogenic microorganism which has been described as growing at temperatures of interest to food production and especially at low temperatures (-2 degrees to 8 degrees C) in storage process. However, the general relationship between the maximum specific growth rate, mumax and temperature has not often been studied for L. monocytogenes in the whole temperature range from minimal to maximal growth temperature. A global analysis of this relationship for temperatures between -2 degrees C and 42 degrees C was therefore done. The global shape of this relationship was that usually observed for microorganisms, especially in the neighbourhood of the optimal temperature, Topt. But a more detailed study showed the existence of a so-called "change temperature", occurring between 10 degrees and 15 degrees C, below which L. monocytogenes grows faster than one would expect. This implies that the minimal growth temperature of both studied strains of L. monocytogenes is lower than expected.

Accuracy of microbial growth predictions with square root and polynomial models

The results of growth predictions using square root and polynomial models published in 14 papers were studied. Errors on quantities of practical interest such as lag time, generation time or the time required to reach a given increase in number of cells, are analyzed. The distribution of these errors was examined with the perspective of the practical use of predictive models in food industry. Highly unsafe predictions and significant average errors were observed in some cases. A good knowledge of predictive models accuracy seems essential for their efficient and safe use, for example to predict the shelf life of a product. Yet, authors generally gave no pragmatic information on such things as the average relative error or the range of errors on predicted variables. Problems of robustness of models when tested in different conditions were noticed, which corroborates the necessity of a systematic validation of models on new data.