Investigations of patients with suspected Mycoplasma pneumoniae infection have been undertaken in England since the early 1970s. M. pneumoniae is a respiratory pathogen that is a common cause of pneumonia and may cause serious sequelae such as encephalitis and has been documented in children with persistent cough. The pathogen is found in all age groups, with higher prevalence in children aged 5–14 years. In England, recurrent epidemic periods have occurred at ~4-yearly intervals. In addition, low-level sporadic infection occurs with seasonal peaks from December to February. Voluntarily reports from regional laboratories and hospitals in England from 1975 to 2015 were collated by Public Health England for epidemiological analysis. Further data pertaining cases of note and specimens submitted to Public Health England from 2005 to 2015 for confirmation, molecular typing is included.

SummaryBackgroundTotal domestic and international funding for malaria is inadequate to achieve WHO global targets in burden reduction by 2030. We describe the trends of investments in malaria-related research in sub-Saharan Africa and compare investment with national disease burden to identify areas of funding strength and potentially neglected populations. We also considered funding for malaria control.MethodsResearch funding data related to malaria for 1997–2013 were sourced from existing datasets, from 13 major public and philanthropic global health funders, and from funding databases. Investments (reported in US$) were considered by geographical area and compared with data on parasite prevalence and populations at risk in sub-Saharan Africa. 45 sub-Saharan African countries were ranked by amount of research funding received.FindingsWe found 333 research awards totalling US$814·4 million. Public health research covered $308·1 million (37·8%) and clinical trials covered $275·2 million (33·8%). Tanzania ($107·8 million [13·2%]), Uganda ($97·9 million [12·0%]), and Kenya ($92·9 million [11·4%]) received the highest sum of research investment and the most research awards. Malawi, Tanzania, and Uganda remained highly ranked after adjusting for national gross domestic product. Countries with a reasonably high malaria burden that received little research investment or funding for malaria control included Central African Republic (ranked 40th) and Sierra Leone (ranked 35th). Congo (Brazzaville) and Guinea had reasonably high malaria mortality, yet Congo (Brazzaville) ranked 38th and Guinea ranked 25th, thus receiving little investment.InterpretationSome countries receive reasonably large investments in malaria-related research (Tanzania, Kenya, Uganda), whereas others receive little or no investments (Sierra Leone, Central African Republic). Research investments are typically highest in countries where funding for malaria control is also high. Investment strategies should consider more equitable research and operational investments across countries to include currently neglected and susceptible populations.FundingRoyal Society of Tropical Medicine and Hygiene and Bill & Melinda Gates Foundation.

c Mycoplasma pneumoniae is a major human respiratory pathogen causing both upper and lower respiratory disease in humans of all ages, and it can also result in other serious extrapulmonary sequelae. A multilocus sequence typing (MLST) scheme for M. pneumoniae was developed based on the sequences of eight housekeeping genes (ppa, pgm, gyrB, gmk, glyA, atpA, arcC, and adk) and applied to 55 M. pneumoniae clinical isolates and the two type strains M129 and FH. A total of 12 sequence types (STs) resulted for 57 M. pneumoniae isolates tested, with a discriminatory index of 0.21 STs per isolate. The MLST loci used in this scheme were shown to be stable in 10 strains following 10 sequential subculture passages. Phylogenetic analysis of concatenated sequences of the eight loci indicated two distinct genetic clusters that were directly linked to multilocus variable-number tandem repeat analysis (MLVA) type. Genetic MLST clustering was confirmed by genomic sequence analysis, indicating that the MLST scheme developed in this study is representative of the genome. Furthermore, this MLST scheme was shown to be more discriminatory than both MLVA and P1 typing for the M. pneumoniae isolates examined, providing a method for further and more detailed analysis of observed epidemic peaks of M. pneumoniae infection. This scheme is supported by a public Web-based database (http://pubmlst.org/mpneumoniae). Mycoplasma pneumoniae is a common cause of communityacquired pneumonia (CAP) transmitted by aerosol or close contact (1). M. pneumoniae may cause other serious extrapulmonary sequelae, such as encephalitis (2). The pathogen is found in all age groups, with a higher prevalence in children age 5 to 14 years (3, 4). Admissions to a United Kingdom hospital in patients with CAP that were attributed to M. pneumoniae were estimated at 18% in 1982 and 4% in 1999 (5). Major increases and decreases in M. pneumoniae infection have occurred periodically in the United Kingdom; historically, epidemics have occurred at approximately 4-year intervals and have lasted 12 to 15 months, concurrent with sporadic infection at a lower level and seasonal peaks from December to February (4, 6). However, globally, peaks of infection have been observed in either summer or autumn, with no obvious explanation for this seasonal variation (7-10).Typing of clinical isolates by molecular methods is of importance for the understanding of the epidemiology of M. pneumoniae infection and for an analysis of endemic outbreaks. It is generally considered that molecular typing of M. pneumoniae is hampered by the fact that the pathogen is a genetically homologous species (11). Initial molecular typing targeted the gene encoding the major surface protein (P1) of M. pneumoniae. PCRrestriction fragment length polymorphism (PCR-RFLP) analysis of the P1 gene, which encodes a major adhesion, is the most common genotyping method. This enables the separation of isolates into two types, 1 and 2 (11-13). More recent studies utilize the repetitive regions, RepMp2/3 and RepMp4, which ...

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Mycoplasma pneumoniae infection can cause pneumonia, particularly in children. Global increase in macrolide-resistant M. pneumoniae is of concern due to limited therapeutic options. We describe the detection of macrolide resistance-conferring mutations in 9.3% of 43 clinical specimens where M. pneumoniae was detected in England and Wales from September 2014-September 2015. This study aims to impact by highlighting the presence of macrolide resistance in M. pneumoniae positive patients, promoting increased clinical vigilance. Macrolide resistance determinationThe Bacteriology Reference Department, Public Health England (PHE), London, receives specimens from England and Wales for M. pneumoniae testing and confirmatory testing. Here we detected M. pneumoniae by qPCR in 60 clinical specimens from 60 patients (Cambridge, Leeds, London, Manchester, Nottingham and Oxford) that were submitted to PHE between 1 September 2014 and 1 September 2015. DNA extractions from specimens, where M. pneumoniae was detected, were screened for point mutations known to confer macrolide resistance. Mutations in domain V of the 23S rRNA were detected by a modified version of the method described by Li et al., 2009 [3], wherein the entire region of interest is amplified and sequenced as one product. Primers used were as follows: forward primer 5'-ATCTCTTGACTGTCTCGGC-3' and reverse primer 5'-TACAACTGGAGCATAAGAGGTG-3'.Of the 60 specimens, 17 (28.3%; 95% confidence interval (CI): 18.4--40.8) contained insufficient DNA to determine macrolide resistance-conferring mutations. Of the remaining 43 specimens mutations in the 23S rRNA known to confer macrolide resistance were found in four (9.3%; 95% CI: 3.1-22.2). Of these 43 specimens, 32 were from a single city in England, Leeds, and a single specimen among these was positive for the mutation, 3.1% (95% CI: 0.01-17.1). The cases identified with point mutations known to confer macrolide-resistant M. pneumoniae were in two women and two men, respectively, aged > 15 to <65 years old. Three were hospitalised with pneumonia (Table) with no known connection between patients.Interestingly, two of the macrolide-resistant cases were patients that had recently arrived from the United States (exact timeline unknown); of which one had received clarithromycin whilst undergoing treatment in the UK. The origins of the infecting M. pneumoniae strains in these two cases may have been external to England and Wales. The other two cases were from separate cities in England. All macrolide resistanceconferring mutations were A2058G (Escherichia coli numbering) point mutation in the 23S rRNA.

Background Each year, billions of US$ are spent globally on infectious disease research and development. However, there is little systematic tracking of global research and development. We present research on investments into infectious diseases research from funders in the G20 countries across an 18-year time period spanning 2000–17, comparing amounts invested for different conditions and considering the global burden of disease to identify potential areas of relative underfunding. Methods The study examined research awards made between 2000 and 2017 for infectious disease research from G20-based public and philanthropic funders. We searched research databases using a range of keywords, and open access data were extracted from funder websites. Awards were categorised by type of science, specialty, and disease or pathogen. Data collected included study title, abstract, award amount, funder, and year. We used descriptive statistics and Spearman's correlation coefficient to investigate the association between research investment and disease burden, using Global Burden of Disease 2017 study data. Findings The final 2000–17 dataset included 94 074 awards for infectious disease research, with a sum investment of $104·9 billion (annual range 4·1 billion to 8·4 billion) and a median award size of $257 176 (IQR 62 562–770 661). Pre-clinical research received $61·1 billion (58·2%) across 70 337 (74·8%) awards and public health research received $29·5 billion (28·1%) from 19 197 (20·4%) awards. HIV/AIDS received $42·1 billion (40·1%), tuberculosis received $7·0 billion (6·7%), malaria received $5·6 billion (5·3%), and pneumonia received $3·5 billion (3·3%). Funding for Ebola virus ($1·2 billion), Zika virus ($0·3 billion), influenza ($4·4 billion), and coronavirus ($0·5 billion) was typically highest soon after a high-profile outbreak. There was a general increase in year-on-year investment in infectious disease research between 2000 and 2006, with a decline between 2007 and 2017. Funders based in the USA provided $81·6 billion (77·8%). Based on funding per 2017 disability-adjusted life years (DALYs), HIV/AIDS received the greatest relative investment ($772 per DALY), compared with tuberculosis ($156 per DALY), malaria ($125 per DALY), and pneumonia ($33 per DALY). Syphilis and scabies received the least relative investment (both $9 per DALY). We observed weak positive correlation (r=0·30) between investment and 2017 disease burden. Interpretation HIV research received the highest amount of investment relative to DALY burden. Scabies and syphilis received the lowest relative funding. Investments for high-threat pathogens (eg, Ebola virus and coronavirus) were often reactive and followed outbreaks. We found little evidence that funding is proactively guided by global burden or pandemic risk. Our findings show how research investments are allocated and how this relates to disease burden and diseases with pandemic potentia...

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Background Mycoplasma hominis is an opportunistic human pathogen, associated with clinically diverse disease. Currently, there is no standardised method for typing M. hominis, which would aid in understanding pathogen epidemiology and transmission. Due to availability and costs of whole genome sequencing and the challenges in obtaining adequate M. hominis DNA, the use of whole genome sequence analysis to provide clinical guidance is unpractical for this bacterial species as well as other fastidious organisms.ResultsThis study identified pan-genome set of 700 genes found to be present in four published reference genomes. A subset of 417 genes was identified to be core genome for 18 isolates and 1 reference. Leave-one-out analysis of the core genes highlighted set of 48 genes that are required to recapture the original phylogenetic relationships observed using whole genome SNP analysis. Three 7-locus MLST schemas with high diversity index (97%) and low dN/dS ratios (0.1, 0.13, and 0.11) were derived that could be used to confer good discrimination between strains and could be of practical use in future studies direct on clinical specimens.ConclusionsThe genes proposed in this study could be utilised to design a cost-effective and rapid PCR-based MLST assay that could be applied directly to clinical isolates, without prior isolation. This study includes additional genomic analysis revealing high levels of genetic heterogeneity among this species. This provides a novel and evidence based approach for the development of MLST schema that accurately represent genomic phylogeny for use in epidemiology and transmission studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3284-z) contains supplementary material, which is available to authorized users.