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The National Collection of Type Cultures (NCTC) was founded on 1 January 1920 in order to fulfil a recognized need for a centralized repository for bacterial and fungal strains within the UK. It is among the longest-established collections of its kind anywhere in the world and today holds approximately 6000 type and reference bacterial strains – many of medical, scientific and veterinary importance – available to academic, health, food and veterinary institutions worldwide. Recently, a collaboration between NCTC, Pacific Biosciences and the Wellcome Sanger Institute established the NCTC3000 project to long-read sequence and assemble the genomes of up to 3000 NCTC strains. Here, at the beginning of the collection’s second century, we introduce the resulting NCTC3000 sequence read datasets, genome assemblies and annotations as a unique, historically and scientifically relevant resource for the benefit of the international bacterial research community.

ObjectivesA Finnish Chlamydia trachomatis (CT) new variant was detected in 2019 that escaped detection in the Hologic Aptima Combo 2 (AC2) assay due to a C1515T mutation in the CT 23S rRNA target region. Reflex testing of CT-negative/CT-equivocal specimens as well as those positive for Neisseria gonorrhoeae (NG) with the Hologic Aptima CT (ACT) assay was recommended to identify any CT variants.MethodsFrom June to October 2019, specimens with discrepant AC2/ACT CT results were submitted to Public Health England and screened for detectable CT DNA using an inhouse real-time (RT)-PCR. When enough DNA was present, partial CT 23S rRNA gene sequencing was performed. Analysis of available relative light units and interpretative data was performed.ResultsA total of 317 discordant AC2/ACT specimens were collected from 315 patients. Three hundred were tested on the RT-PCR; 53.3% (n=160) were negative and 46.7% (n=140) were positive. Due to low DNA load in most specimens, sequencing was successful for only 36 specimens. The CT 23S rRNA wild-type sequence was present in 32 specimens, and two variants with C1514T or G1523A mutation were detected in four specimens from three patients. Of the discordant specimens with NG interpretation, 36.6% of NG-negative/CT-negative AC2 specimens had detectable CT DNA on the inhouse RT-PCR vs 53.3% of NG-positive/CT-negative specimens.ConclusionsNo widespread dissemination of AC2 diagnostic-escape CT variants has occurred in England. We however identified the impact of NG positivity on the discordant AC2/ACT specimens; a proportion appeared due to NG positivity and the associated NG signal, rather than any diagnostic-escape variants or low DNA load. Several patients with gonorrhoea may therefore receive false-negative AC2 CT results. Single diagnostic targets and multiplex diagnostic assays have their limitations such as providing selection pressure for escape mutants and potentially reduced sensitivity, respectively. These limitations must be considered when establishing diagnostic pathways.

We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.

Kocuria rosea is a Gram-positive coccus found in the environment and within normal human skin microbiota, and more recently, it has been potentially implicated as an opportunistic pathogen. Here, we describe the genome sequences of five strains of K. rosea (NCTC2676, NCTC7514, NCTC7512, NCTC7528, and NCTC7511).

Raoultella terrigena is a bacterial species associated with soil and aquatic environments; however, sporadic cases of opportunistic disease in humans have been reported. Here, we report the first two complete genome sequences from clinical strains isolated from human sources that have been deposited in the National Collection of Type Cultures (NCTC).

Haemophilus haemolyticus is a Gram-negative bacterium that is a commensal of the respiratory tract in humans. Here, we report the complete genome sequence available for Haemophilus haemolyticus strain NCTC 10839, which was originally isolated from the nasopharynx of a child.

The sixth global cholera pandemic lasted from 1899 to 1923. However, despite widespread fear of the disease and of its negative effects on troop morale, very few soldiers in the British Expeditionary Forces contracted cholera between 1914 and 1918. Here, we have revived and sequenced the genome of NCTC 30, a 102-year-old Vibrio cholerae isolate, which we believe is the oldest publicly available live V. cholerae strain in existence. NCTC 30 was isolated in 1916 from a British soldier convalescent in Egypt. We found that this strain does not encode cholera toxin, thought to be necessary to cause cholera, and is not part of V. cholerae lineages responsible for the pandemic disease. We also show that NCTC 30, which predates the introduction of penicillin-based antibiotics, harbours a functional β-lactamase antibiotic resistance gene. Our data corroborate and provide molecular explanations for previous phenotypic studies of NCTC 30 and provide a new high-quality genome sequence for historical, non-pandemic V. cholerae .

The National Collection of Type Cultures (NCTC) is the world’s oldest bacterial collection that was specifically established to provide strains globally to support scientific research. In addition to the general catalogue NCTC has a fully curated bacteriophage and plasmid archive that to date has not recently been made available to the wider scientific community. The NCTC bacteriophage collection consists of over 100 bacteriophage and their corresponding bacterial hosts which were originally deposited primarily for their value in bacterial typing. The collection consists of bacteriophage from the following hosts: Streptococcus agalactiae, Staphylococcus aureus, Escherichia coli and Campylobacter. The NCTC Datta plasmid collection is a curated collection of over 500 unique plasmids which were originally curated to examine the biology of plasmid transfer between and within bacterial strains. The NCTC bacteriophage collection is currently being fully characterised using a range of modern methods including genomic sequencing and electron microscopy. The plasmid collection is also being characterised using genomic sequencing and restriction digest profiles. It is intended that once characterised and rebanked both the plasmid and bacteriophage collections will be made available in 2019 to scientists to support research and development. The NCTC bacteriophage and plasmid collections will both be dynamic, representing an active repositories into which microbiologists can deposit phages and plasmids to support accessibility and reproducibility in science.

Salmonellae are a significant cause of morbidity and mortality globally. Here, we report the first complete genome sequence for Salmonella enterica subsp. enterica serovar Java strain NCTC5706. This strain is of historical significance, having been isolated in the pre-antibiotic era and was deposited into the National Collection of Type Cultures in 1939.

Qaisar Maqbool,1 Mudassar Nazar,1 Sania Naz,2 Talib Hussain,3 Nyla Jabeen,4 Rizwan Kausar,5 Sadaf Anwaar,4 Fazal Abbas,6,7 Tariq Jan6 1Department of Biotechnology, Virtual University of Pakistan, Lahore, Pakistan; 2Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan; 3National Institute of Vacuum Science and Technology (NINVAST), Islamabad, Pakistan; 4Department of Biotechnology and Bioinformatics Lab., International Islamic University, Islamabad, Pakistan; 5Department of Chemistry, University of Sargodha, Sargodha, Pakistan; 6Department of Physics, International Islamic University, Islamabad, Pakistan; 7Interdisciplinary Research Organization, University of Chakwal (UOC), Chakwal, Pakistan Abstract: This article reports the green fabrication of cerium oxide nanoparticles (CeO2 NPs) using Olea europaea leaf extract and their applications as effective antimicrobial agents. O. europaea leaf extract functions as a chelating agent for reduction of cerium nitrate. The resulting CeO2 NPs exhibit pure single-face cubic structure, which is examined by X-ray diffraction, with a uniform spherical shape and a mean size 24 nm observed through scanning electron microscopy and transmission electron microscopy. Ultraviolet-visible spectroscopy confirms the characteristic absorption peak of CeO2 NPs at 315 nm. Fourier transform infrared spectroscopy reflects stretching frequencies at 459 cm-1, showing utilization of natural components for the production of NPs. Thermal gravimetric analysis predicts the successful capping of CeO2 NPs by bioactive molecules present in the plant extract. The antimicrobial studies show significant zone of inhibition against bacterial and fungal strains. The higher activities shown by the green synthesized NPs than the plant extract lead to the conclusion that they can be effectively used in biomedical application. Furthermore, reduction of cerium salt by plant extract will reduce environmental impact over chemical synthesis. Keywords: XRD, SEM, TEM, FTIR, antibacterial, antifungal, nanomedicine, green fabrication

Plesiomonas shigelloides is a Gram-negative rod within the Enterobacteriaceae family. It is a gastrointestinal pathogen of increasing notoriety, often associated with diarrheal disease. P. shigelloides is waterborne, and infection is often linked to the consumption of seafood. Here, we describe the first complete genome for P. shigelloides type strain NCTC10360.

Neisseria weaveri is a commensal organism of the canine oral cavity and an occasional opportunistic human pathogen which is associated with dog bite wounds. Here we report the first complete genomic sequence of the N. weaveri NCTC13585 (CCUG30381) strain, which was originally isolated from a patient with a canine bite wound.

We study a traditional one-dimensional model of biofilm formation. It includes biofilm growth due to substrate consumption and biomass loss due to natural decay and detachment. The substrate diffuses from the surrounding aqueous phase into the biofilm. Its consumption by the microbes is described by the steady state diffusion-reaction model with Monod kinetics. Overall, this leads to an initial value problem for biofilm thickness that is coupled with a two-point boundary value problem for the growth limiting substrate. In a first study, we derive a simple, easy to use analytical approximation for the diffusive substrate flux across the water-biofilm interface. Starting point for this is the homotopy perturbation method, which, however, converges poorly for realistic biofilm parameters due to the particular non- linearity of the Monod kinetics. We overcome this difficulty by observing that the biofilm thickness is a small parameter, which allows us to apply a perturbation argument to the infinite series representation of the homotopy solution. The analytical approximation that we derive with this approach is verified quantitatively against a numerical solution of the full boundary value problem. A second aspect of the thesis the role of detachment for the long term behavior of the biofilm model in a narrow conduit, in particular with a view on bioclogging of the channel. We compare four heuristic different detachment rate functions, three of which have been used in the literature before and one is suggested here. Two of these detachment rates consider only material properties of the biofilm but are independent of the hydrodynamic shear forces, while the other two also take flow effects into account. Using analytical and numerical techniques, we find that persistence and the long term behavior of the system can depend critically on the flow regime as well as on the expression used to model biomass detachment. Finally, using a simple upscaling technique, we derive from our meso-scopic one-dimensional biofilm model a macroscopic model for a porous medium biofilm reactor under a convection dominated, laminar regime. The upscaled model is a stiff quasi-linear hyperbolic system. Using characteristic theory we describe the solutions qualitatively. In numerical simulations we investigate the role of meso-scopic biofilm detachment for macro-scopic system. We find that the reactor performance is largely independent of the particular choice of meso-scopic detachment function. We study a traditional one-dimensional model of biofilm formation. It includes biofilm growth due to substrate consumption and biomass loss due to natural decay and detachment. The substrate diffuses from the surrounding aqueous phase into the biofilm. Its consumption by the microbes is described by the steady state diffusion-reaction model with Monod kinetics. Overall, this leads to an initial value problem for biofilm thickness that is coupled with a two-point boundary value problem for the growth limiting substrate.