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2. Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium

Author

Shaw, David, Abad, Raquel, Amin-Chowdhury, Zahin, Bautista, Adriana, Bennett, Desiree, Broughton, Karen, Cao, Bin, Casanova, Carlo, Choi, Eun Hwa, Chu, Yiu-Wai, Claus, Heike, Coelho, Juliana, Corcoran, Mary, Cottrell, Simon, Cunney, Robert, Cuypers, Lize, Dalby, Tine, Davies, Heather, de Gouveia, Linda, Deghmane, Ala-Eddine, Demczuk, Walter, Desmet, Stefanie, Domenech, Mirian, Drew, Richard, du Plessis, Mignon, Duarte, Carolina, Erlendsdóttir, Helga, Fry, Norman K, Fuursted, Kurt, Hale, Thomas, Henares, Desiree, Henriques-Normark, Birgitta, Hilty, Markus, Hoffmann, Steen, Humphreys, Hilary, Ip, Margaret, Jacobsson, Susanne, Johnson, Christopher, Johnston, Jillian, Jolley, Keith A, Kawabata, Aníbal, Kozakova, Jana, Kristinsson, Karl G, Krizova, Pavla, Kuch, Alicja, Ladhani, Shamez, Lâm, Thiên-Trí, León, María Eugenia, Lindholm, Laura, Litt, David, Maiden, Martin C J, Martin, Irene, Martiny, Delphine, Mattheus, Wesley, McCarthy, Noel D, Meehan, Mary, Meiring, Susan, Mölling, Paula, Morfeldt, Eva, Morgan, Julie, Mulhall, Robert, Muñoz-Almagro, Carmen, Murdoch, David, Murphy, Joy, Musilek, Martin, Mzabi, Alexandre, Novakova, Ludmila, Oftadeh, Shahin, Perez-Argüello, Amaresh, Pérez-Vázquez, Maria, Perrin, Monique, Perry, Malorie, Prevost, Benoit, Roberts, Maria, Rokney, Assaf, Ron, Merav, Sanabria, Olga Marina, Scott, Kevin J, Sheppard, Carmen, Siira, Lotta, Sintchenko, Vitali, Skoczyńska, Anna, Sloan, Monica, Slotved, Hans-Christian, Smith, Andrew J, Steens, Anneke, Taha, Muhamed-Kheir, Toropainen, Maija, Tzanakaki, Georgina, Vainio, Anni, van der Linden, Mark P G, van Sorge, Nina M, Varon, Emmanuelle, Vohrnova, Sandra, von Gottberg, Anne, Yuste, Jose, Zanella, Rosemeire, Zhou, Fei, and Brueggemann, Angela B

Published
2023
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7. Changes in the incidence of invasive disease due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis during the COVID-19 pandemic in 26 countries and territories in the Invasive Respiratory Infection Surveillance Initiative: a prospective analysis of surveillance data

Author

Brueggemann, Angela B, Jansen van Rensburg, Melissa J, Shaw, David, McCarthy, Noel D, Jolley, Keith A, Maiden, Martin C J, van der Linden, Mark P G, Amin-Chowdhury, Zahin, Bennett, Désirée E, Borrow, Ray, Brandileone, Maria-Cristina C, Broughton, Karen, Campbell, Ruth, Cao, Bin, Casanova, Carlo, Choi, Eun Hwa, Chu, Yiu Wai, Clark, Stephen A, Claus, Heike, Coelho, Juliana, Corcoran, Mary, Cottrell, Simon, Cunney, Robert J, Dalby, Tine, Davies, Heather, de Gouveia, Linda, Deghmane, Ala-Eddine, Demczuk, Walter, Desmet, Stefanie, Drew, Richard J, du Plessis, Mignon, Erlendsdottir, Helga, Fry, Norman K, Fuursted, Kurt, Gray, Steve J, Henriques-Normark, Birgitta, Hale, Thomas, Hilty, Markus, Hoffmann, Steen, Humphreys, Hilary, Ip, Margaret, Jacobsson, Susanne, Johnston, Jillian, Kozakova, Jana, Kristinsson, Karl G, Krizova, Pavla, Kuch, Alicja, Ladhani, Shamez N, Lâm, Thiên-Trí, Lebedova, Vera, Lindholm, Laura, Litt, David J, Martin, Irene, Martiny, Delphine, Mattheus, Wesley, McElligott, Martha, Meehan, Mary, Meiring, Susan, Mölling, Paula, Morfeldt, Eva, Morgan, Julie, Mulhall, Robert M, Muñoz-Almagro, Carmen, Murdoch, David R, Murphy, Joy, Musilek, Martin, Mzabi, Alexandre, Perez-Argüello, Amaresh, Perrin, Monique, Perry, Malorie, Redin, Alba, Roberts, Richard, Roberts, Maria, Rokney, Assaf, Ron, Merav, Scott, Kevin J, Sheppard, Carmen L, Siira, Lotta, Skoczyńska, Anna, Sloan, Monica, Slotved, Hans-Christian, Smith, Andrew J, Song, Joon Young, Taha, Muhamed-Kheir, Toropainen, Maija, Tsang, Dominic, Vainio, Anni, van Sorge, Nina M, Varon, Emmanuelle, Vlach, Jiri, Vogel, Ulrich, Vohrnova, Sandra, von Gottberg, Anne, Zanella, Rosemeire C, and Zhou, Fei

Published
2021
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13. Highly Pathogenic Clone of Shiga Toxin--Producing Escherichia coli O157:H7, England and Wales

Author

Byrne, Lisa, Dallman, Timothy J., Adams, Natalie, Mikhail, Amy F.W., McCarthy, Noel, and Jenkins, Claire

Subjects
Escherichia coli -- Research, DNA sequencing -- Usage, Signs and symptoms -- Research, Health
Abstract

Shiga toxin-producing Escherichia coli (STEC) O157:H7 cause a wide range of gastrointestinal symptoms, including mild gastroenteritis, abdominal pain, vomiting, and bloody diarrhea (1). A subset of patients, most commonly the [...]

Published
2018
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14. Application of sequence typing to the epidemiology of Campylobacter jejuni

Author

McCarthy, Noel and Maiden, Martin

Subjects
616.9
Abstract

The bacterium Campylobacter jejuni is responsible for a substantial burden of human disease. It has a wide host and environmental distribution. The ecology in non-human hosts has been studied, in particular for farm animals, but the relationship between different host and environmental niches, including the extent to which host and geography are associated with genetic differentiation, is uncertain. Open epidemiological questions include the largely unexplained summer peaks in many temperate countries, apparent paucity of outbreaks despite a high incidence of foodborne infection, and uncertainty in the quantitative contributions of different sources to human infection. Bacterial subtyping has not made a substantial contribution to the ecology or epidemiology of this species. This thesis applied a housekeeping gene multilocus sequence typing scheme, complemented with more variable antigen genes, in epidemiological and ecological studies of C. jejuni. These studies identified a large contribution of one clonal group to the high level of human infection during summer along with a similar seasonal rise in relative prevalence for this Glade in poultry meat, and the association of other phenotypic characteristics with the Glade. A lack of geographical variation between distant populations within England contrasted with substantial differences at international level. Genetic differentiation by host species exceeded geographic and temporal effects and showed the potential of using multilocus genotype to attribute human infection to animal host sources. Recombination played a major role in the generation of this genetic differentiation, which finding informed the use of alleles rather than summary measures of genotype in population assignment of C. jejuni. Using fine typing with porA and flaA gene fragments to produce higher discrimination than previously applied allowed the identification of genotypic clusters, demonstrated emergent clades within the poultry industry and human disease, and confirmed empirically the predictions from theoretical work that even more highly discriminatory methods will be needed to reliably identify outbreaks and their specific source using genotype. This work has thus exploited the of integration multilocus sequencing in studies of the epidemiology and ecology of C. jejuni, developed analytical approaches for this application, and identified some limitations and the extent to which these may be tractable with more extensive sequence data and further development of analytical approaches.

Published
2008

17. Water Effective Diffusion Coefficient in Dairy Powder Calculated by Digital Image Processing and through Machine Learning Algorithms of CLSM Micrographs.

Author

Maidannyk, Valentyn A., Simonov, Yuriy, McCarthy, Noel A., and Ho, Quang Tri

Subjects
MACHINE learning, DIGITAL image processing, DIFFUSION coefficients, DIFFUSION measurements, IMAGE analysis, POWDERS
Abstract

Rehydration of dairy powders is a complex and essential process. A relatively new quantitative mechanism for monitoring powders' rehydration process uses the effective diffusion coefficient. This research focused on modifying a previously used labor-intensive method that will be able to automatically measure the real-time water diffusion coefficient in dairy powders based on confocal microscopy techniques. Furthermore, morphological characteristics and local hydration of individual particles were identified using an imaging analysis procedure written in Matlab©—R2023b and image analysis through machine learning algorithms written in Python™-3.11. The first model includes segmentation into binary images and labeling particles during water diffusion. The second model includes the expansion of data set selection, neural network training and particle markup. For both models, the effective diffusion follows Fick's second law for spherical geometry. The effective diffusion coefficient on each particle was computed from the dye intensity during the rehydration process. The results showed that effective diffusion coefficients for water increased linearly with increasing powder particle size and are in agreement with previously used methods. In summary, the models provide two independent machine measurements of effective diffusion coefficient based on the same set of micrographs and may be useful in a wide variety of high-protein powders. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Shedding and exclusion from childcare in children with Shiga toxin-producing Escherichia coli , 2018–2022.

Author

Vusirikala, Amoolya, Rowell, Sam, Dabke, Girija, Fox, Georgina, Bell, Jade, Manuel, Rohini, Jenkins, Claire, Love, Nicola, McCarthy, Noel, Sumilo, Dana, and Balasegaram, Sooria

Abstract

Excluding children with Shiga toxin-producing Escherichia coli (STEC) from childcare until microbiologically clear of the pathogen, disrupts families, education, and earnings. Since PCR introduction, non-O157 STEC serotype detections in England have increased. We examined shedding duration by serotype and transmission risk, to guide exclusion advice. We investigated STEC cases aged <6 years, residing in England and attending childcare, with diarrhoea onset or sample date from 31 March 2018 to 30 March 2022. Duration of shedding was the interval between date of onset or date first positive specimen and earliest available negative specimen date. Transmission risk was estimated from proportions with secondary cases in settings attended by infectious cases. There were 367 cases (STEC O157 n  = 243, 66.2%; STEC non-O157 n  = 124, 33.8%). Median shedding duration was 32 days (IQR 20–44) with no significant difference between O157 and non-O157; 2% (n  = 6) of cases shed for ≥100 days. Duration of shedding was reduced by 17% (95% CI 4–29) among cases reporting bloody diarrhoea. Sixteen settings underwent screening; four had secondary cases (close contacts' secondary transmission rate = 13%). Shedding duration estimates were consistent with previous studies (median 31 days, IQR 17–41). Findings do not warrant guidance changes regarding exclusion and supervised return of prolonged shedders, despite serotype changes. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Health inequalities in infectious diseases: a systematic overview of reviews

Author

Ayorinde, Abimbola, primary, Ghosh, Iman, additional, Ali, Ifra, additional, Zahair, Iram, additional, Olarewaju, Olajumoke, additional, Singh, Megha, additional, Meehan, Edward, additional, Anjorin, Seun Stephen, additional, Rotheram, Suzanne, additional, Barr, Ben, additional, McCarthy, Noel, additional, and Oyebode, Oyinlola, additional

Published
2023
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22. Measuring pH of skim milk and milk permeate at ultra-high temperatures at laboratory and pilot scale

Author

Aydogdu, Tugce, O'Mahony, James A., Huppertz, Thom, Magan, Jonathan B., McCarthy, Noel A., Aydogdu, Tugce, O'Mahony, James A., Huppertz, Thom, Magan, Jonathan B., and McCarthy, Noel A.

Abstract

Changes in the pH of skim milk and skim milk ultrafiltration permeate on heating from 25 to 140 °C were examined. Results showed that the decrease in pH with increase in temperature up to 140 °C was not linear. Hydrogen ion release due to changes in the milk mineral balance were responsible for the reduction in pH with increase in temperature. The presence of milk proteins offered little buffering against the drop in pH. The precipitation of calcium phosphate resulted in sediment in milk permeate heated above ∼70 °C, but this did not occur in skim milk, with the pH remaining lower in milk permeate after heat treatment when measured at 25 °C. This study has shown that in-line pH measurements of milk at ultra-high temperatures is feasible, and could prove useful at laboratory and pilot-scale for studying interactions within, and stability of, more complex formulations with added minerals.

Published
2023

25. pH, the Fundamentals for Milk and Dairy Processing: A Review.

Author

Aydogdu, Tugce, O'Mahony, James A., and McCarthy, Noel A.

Subjects
DAIRY processing, MEASUREMENT of viscosity, ENERGY industries, DAIRY industry, MILK quality, MILKING, CASEINS
Abstract

The ability to measure and capture real-time unit operational data has significant benefits during dairy processing, whether it is the basics, such as measuring temperature, pressure, and flow rates, or more recent developments in the case of in-line viscosity and product-compositional measurements. This rapid data collection has helped increase profitability by reducing energy costs, minimizing product loss, and allowing automated control. Advances in technology have allowed for in-line measurements of the composition and some physical attributes such as particle size and viscosity; however, an attribute that spans both compositional and physical attributes is pH, directly influenced by composition but also environments, such as temperature and dry matter content. pH is measured for a plethora of reasons, such as a measure of milk quality (microbial spoilage), acidification of casein, cheese production, maintaining optimum conditions during protein hydrolysis, etc. However, very little is published on the fundamentals of pH and pH measurement in dairy processing; rather, it is usually a cause-and-effect phenomenon. This review visits one of the oldest analytical considerations in the dairy industry and re-examines how it is affected by product composition and processing conditions. [ABSTRACT FROM AUTHOR]

Published
2023
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31. Integration of genomic and other epidemiologic data to investigate and control a cross-institutional outbreak of Streptococcus pyogenes

Author

Chalker, Victoria J., Smith, Alyson, Al-Shahib, Ali, Botchway, Stella, Macdonald, Emily, Daniel, Roger, Phillips, Sarah, Platt, Steven, Doumith, Michel, Tewolde, Rediat, Coelho, Juliana, Jolley, Keith A., Underwood, Anthony, and McCarthy, Noel D.

Subjects
Genomics -- Analysis -- Health aspects -- Surveys, Genomes -- Analysis -- Health aspects -- Surveys, Infection -- Analysis -- Health aspects -- Surveys, Single nucleotide polymorphisms -- Analysis -- Health aspects -- Surveys, Health
Abstract

The reported annual incidence of invasive group A Streptococcus (iGAS) infection in industrialized countries is ≅ 3 cases per 100,000 persons per year (1-3). Incidence is 3-fold higher among persons [...]

Published
2016
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33. Changes in Serogroup and Genotype Prevalence Among Carried Meningococci in the United Kingdom During Vaccine Implementation

Author

Ibarz-Pavón, Ana Belén, MacLennan, Jenny, Andrews, Nicholas J., Gray, Stephen J., Urwin, Rachel, Clarke, Stuart C., Walker, A. Mark, Evans, Meirion R., Kroll, J. Simon, Neal, Keith R., Ala'Aldeen, Dlawer, Crook, Derrick W., Cann, Kathryn, Harrison, Sarah, Cunningham, Richard, Baxter, David, Kaczmarski, Edward, McCarthy, Noel D., Jolley, Keith A., Cameron, J. Claire, Stuart, James M., and Maiden, Martin C. J.

Published
2011
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35. Epidemiology and genomic analysis of Shiga toxin-producing Escherichia coli clonal complex 165 in the UK

Author

Rodwell, Ella V, Vishram, Bhavita, Smith, Robert, Browning, Lynda, Smith-Palmer, Alison, Allison, Lesley, Holmes, Anne, Godbole, Gauri, McCarthy, Noel, Dallman, Timothy J, Jenkins, Claire, IRAS OH Epidemiology Microbial Agents, and IRAS OH Epidemiology Microbial Agents

Subjects
Microbiology (medical), renal failure, whole-genome sequencing, haemolytic uraemic syndrome, complex STEC infection, General Medicine, Microbiology, QR
Abstract

Introduction. Shiga toxin-producing Escherichia coli (STEC) is a zoonotic, foodborne gastrointestinal pathogen that has the potential to cause severe clinical outcomes, including haemolytic uraemic syndrome (HUS). STEC-HUS is the leading cause of renal failure in children and can be fatal. Over the last decade, STEC clonal complex 165 (CC165) has emerged as a cause of STEC-HUS. Gap Statement. There is a need to understand the pathogenicity and prevalence of this emerging STEC clonal complex in the UK, to facilitate early diagnosis, improve clinical management, and prevent and control outbreaks. Aim. The aim of this study was to characterize CC165 through identification of virulence factors (VFs) and antimicrobial resistance (AMR) determinants in the genome and to integrate the genome data with the available epidemiological data to better understand the incidence and pathogenicity of this clonal complex in the UK. Methodology. All isolates belonging to CC165 in the archives at the UK public health agencies were sequenced and serotyped, and the virulence gene and AMR profiles were derived from the genome using PHE bioinformatics pipelines and the Centre for Genomic Epidemiology virulence database. Results. There were 48 CC165 isolates, of which 43 were STEC, four were enteropathogenic E. coli (EPEC) and one E. coli . STEC serotypes were predominately O80:H2 (n=28), and other serotypes included O45:H2 (n=9), O55:H9 (n=4), O132:H2 (n=1) and O180:H2 (n=1). All but one STEC isolate had Shiga toxin (stx) subtype stx2a or stx2d and 47/48 isolates had the eae gene encoding intimin involved in the intimate attachment of the bacteria to the human gut mucosa. We detected extra-intestinal virulence genes including those associated with iron acquisition (iro) and serum resistance (iss), indicating that this pathogen has the potential to translocate to extra-intestinal sites. Unlike other STEC clonal complexes, a high proportion of isolates (93%, 40/43) were multidrug-resistant, including resistance to aminoglycosides, beta-lactams, chloramphenicol, sulphonamides, tetracyclines and trimethoprim. Conclusion. The clinical significance of this clonal complex should not be underestimated. Exhibiting high levels of AMR and a combination of STEC and extra-intestinal pathogenic E. coli (ExPEC) virulence profiles, this clonal complex is an emerging threat to public health.

Published
2021

46. Health Effects Of Prisons

Author

Smyth, Bobby P., Langkamp, Herbert, Schmid, Matthias L., Green, Stephen T., McKendrick, Michael W., and McCarthy, Noel

Published
2000

47. Duck liver-associated outbreak of Campylobacter infection among humans, United Kingdom, 2011

Author

Abid, Muhammad, Wimalarathna, Helen, Mills, Janette, Saldana, Luisa, Pang, Winnie, Richardson, Judith F., Maiden, Martin C.J., and McCarthy, Noel D.

Subjects
Gastroenteritis -- Analysis -- Health aspects, Liver -- Analysis -- Health aspects, Food contamination -- Analysis -- Health aspects, Health
Abstract

Although bacteria in the genus Campylobacter commonly cause gastroenteritis, identified outbreaks are relatively rare. In England and Wales, 21 identified campylobacteriosis outbreaks during 1992-1994 (1) and 50 during 1995-1999 (2) [...]

Published
2013
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