Rapid communications Shigellosis in refugees , Austria , July to November 2015

We report on a cluster of shigellosis including 21 cases in refugees and two in local residents who worked in refugee transit centres, detected in Austria in 2015, between calendar weeks 29 and 47. The species isolated from the cluster cases, including one mixed infection, were S. sonnei (n = 13), S. flexneri (n = 10) and S. boydii (n = 1). Eleven of 18 tested isolates were extended spectrum beta-lactamase (ESBL)-positive, including five of six ciprofloxacin-resistant and three azithromycin-resistant isolates.

We report on a cluster of shigellosis including 21 cases in refugees and two in local residents who worked in refugee transit centres, detected in Austria in 2015, between calendar weeks 29 and 47.The species isolated from the cluster cases, including one mixed infection, were S. sonnei (n = 13), S. flexneri (n = 10) and S. boydii (n = 1).Eleven of 18 tested isolates were extended spectrum beta-lactamase (ESBL)-positive, including five of six ciprofloxacin-resistant and three azithromycin-resistant isolates.
Since June 2015, there has been an increase in the number of refugees arriving in Austria seeking asylum (monthly average approximately 9,000 [1] or transiting through Austria (approximately one million since July, personal communication, Austrian office, International Organization of Migration, November 2015) to seek asylum elsewhere.We report on the occurrence of 23 cases of shigellosis in 21 refugees and two Austrian residents, identified between 18 July and 18 November 2015 (Figure 1).No cases of shigellosis in refugees were reported before July 2015.
From January until June 2015, 13 cases of shigellosis have been reported among Austrian citizens and 35 cases from July until November; this does not exceed the expected case number compared with 2014.In 2014 in Austria, four cases were identified among non-Austrian citizens from non-European Union (EU) countries i.e. from Serbia and Turkey, respectively.
The cases in refugees presented here were detected during patients' consultation at the medical care facility located in the transit centres (passive case finding) or during the entry health examination at the reception centres, which is compulsory for asylum seekers in Austria (active case finding).Transit centres usually host refugees for a short time (few days), whereas reception centres accommodate asylum seekers for up to several months until long-term housing becomes available.In these centres, there is no screening programme in place for Shigella carriage or other enteric pathogens.
The Table displays the cases by age, date, Austrian province and location of detection, country of origin, epidemiological link and Shigella species with antimicrobial susceptibility.The age distribution among cases was from 1 to 65 years; 16/23 cases were under 10 years old, three cases were in adolescents and four in adults; 15 cases were male.There were 14 cases from Afghanistan including three cases in under fiveyear-olds, five from Syria, including one child under five years old, and two from Iraq.
Three unrelated cases (Case 11, 21 and 23) were each identified in different reception centres, of which one has a syndromic surveillance system in place, including also the syndrome 'watery diarrhoea' (Tyrol: 1 case; Vienna: 2 cases).The remaining 20 cases were identified in eight transit centres (TC) for refugees in six of the nine Austrian provinces (Vienna: 6 cases in 3 TCs; Burgenland and Upper Austria: 4 cases in 1 TC, respectively; Lower Austria: 2 cases in 1 TC; Carinthia: 3 cases in 1 TC; Styria: 1 case in 1 TC) (Figure 2).The 21 shigellosis cases in refugees were caused by S. sonnei (n = 11), S. flexneri (n = 9) and S. boydii (n = 1).
One of the two affected Austrian residents, a professional cleaner (Case 12) developed diarrhoea one day after cleaning a refugee transit centre's toilet using a high-pressure cleaner without wearing personal protective equipment (PPE).This case tested positive for S. sonnei and S. flexneri and was the first known case associated with centre F (Table ).An infection with S. sonnei was detected in a translator (Case 16) working at a transit centre; the source of infection for this case is unknown.
Two cases originating from Afghanistan (Cases 1 and 2) were linked by time (i.e.date of detection ≤ three days apart) and place (i.e.stay in the same transit center) and positive for S. sonnei.Two further cases coming from Afghanistan and Iraq (Cases 3 and 4) were epidemiologically linked, but infected with different Shigella species (Table ).Another two cases belonging to one family from Afghanistan (Cases 14 and 15) were infected with S. sonnei.

Testing of antimicrobial susceptibility
A total of 18 Shigella initial isolates were available for in vitro susceptibility testing: nine isolates of S. sonnei, eight of S. flexneri and one isolate of S. boydii.Resistance testing was performed on Mueller Hinton E agar (bioMérieux, Marcy l'Etoile) using Etest strips (bioMérieux) as described elsewhere [2].Of the 18 isolates tested, 11 expressed extended-spectrum betalactamase (ESBL) (S. flexneri 7/8; S. sonnei 3/9; S. boydii 1/1).Six isolates were resistant to ciprofloxacin.All four ciprofloxacin-resistant S. flexneri isolates were also ESBL-positive, as was the ciprofloxacin-resistant S. boydii; the S. sonnei isolate resistant to ciprofloxacin was ESBL-negative.
In the absence of criteria for Shigella spp.concerning azithromycin resistance by the European Committee on Antimicrobial Susceptibility Testing (EUCAST), we used criteria published for Salmonella enterica serovar Typhi (resistant: minimum inhibitory concentration (MIC) ≥ 32 µg/ml) [3].

Figure 1
Cases of shigellosis in refugees and in two Austrian residents, by calendar week of diagnosis, Austria, 18   Of the 18 isolates tested, three (S.flexneri, (n=2) from Syrian refugees; S. boydii (n=1) from an Afghan refugee) showed resistance against azithromycin (all in addition to their ESBL positivity, and two in addition to ciprofloxacin resistance).

Discussion and conclusion
Shigellosis is an acute infection of the intestine caused by bacteria of the genus Shigella, i.e. S. dysenteriae, S. flexneri, S. boydii and S. sonnei [4].In the World Health Organization (WHO) Eastern Mediterranean Region, shigellosis is recognised as one of the major causes of persistent diarrhoea [5,6].Epidemics of shigellosis have repeatedly affected sub-Saharan Africa, Central America and south/south-east Asia, often hitting areas of political upheaval and natural disaster [7].In western European countries transmission is limited to groups with close contact often with a primary case infected during foreign travel.Refugees are at increased risk of infectious disease primarily due to their vulnerability, poor hygiene condition, and overcrowding in reception or transit centres.Shigellosis is a well-known problem in these settings [8][9][10].We discovered high rates of antimicrobial resistance in all Shigella species isolated from the recently arrived refugees, which physicians should be aware of.Azithromycin is recommended by the American Academy of Paediatrics for treatment of shigellosis in children and by the WHO as a second-line treatment in adults [7].So far, the intercontinental spread of azithromycin-resistant Shigella mainly affected men who have sex with men [11][12][13].The acquisition and expression of ESBLs is not unusual for Shigella.Our findings on ESBL-positivity in 11 of 18 tested isolates from refugees originating from Afghanistan, Iraq and Syria make antimicrobial susceptibility testing in this population indispensable.
In Austria in 2015, an additional 40 S. sonnei isolates were documented without any known refugee-association; only five of them were ESBL-producing; 13 were  Shigellosis among refugees has previously been observed in similar settings globally [10,14,15].Carriers and infected persons who do not clean their hands thoroughly with water and soap after defecation are the main source of Shigella spread.With the arrival of the northern hemisphere winter, risks posed by pathogens, whose spread is facilitated by overcrowding, insufficient sanitary facilities and lower temperatures will increase [16].Unless hygiene measures are sufficiently applied in transit centres and reception centres, more cases of shigellosis may be observed among refugees who have recently arrived in the EU.Therefore, an organised effort to promote personal hygiene concurring with refugees' cultural practice, such as washing after defecation or use of particular types of latrines, is the most important control measure to decrease faecal-oral transmission in refugee centres.In addition, it is important to keep in mind that according to a recent risk assessment published by the European Centre for Disease Prevention and Control (ECDC), 'refugees are vulnerable to infectious diseases because of the specific circumstances under which they live and therefore they require special attention' [17].

Macrolide resistance determination
The

Background
Mycoplasma pneumoniae can be isolated from patients with lower respiratory tract infection, including pneumonia, and has also been associated with prolonged persistent cough and exacerbation of asthma [4].M. pneumoniae infections may manifest infrequently as extra-pulmonary sequelae after the onset of or even in the absence of respiratory illness [5]; including encephalitis [6], dermatological manifestations such as Stevens-Johnson syndrome [7], and haemolytic anaemia [8].Asymptomatic carriage of M. pneumoniae has been documented in nasopharyngeal swabs at low levels in England, e.g. at 0.25% based on PCR in a 2001 carriage study [9], however, a study from the Netherlands reported a much higher carriage rate (21.2%) [10].In England and Wales, M. pneumoniae infection can be found in all age groups, with a higher prevalence in children of school age [9].In England and Wales, seasonal peaks of infection are detected from December to February each year with epidemics at approximately four-yearly intervals, lasting 12 to 15 months [9].A large increase in reported M. pneumoniae cases was documented in several European countries, including England and Wales, in 2011 [11].

Discussion
In the past 15 years, a significant increase in macrolideresistant M. pneumoniae has been reported globally, of increasing concern and importance to the international community [12].In Asia, resistance rates of over 90% have been reported [13], particularly in China, whereas in Europe and North America resistance rates of up to 25% have been documented [14,15].Macrolideresistant strains of M. pneumoniae have not been documented to show cross-resistance to other classes of antibiotics i.e. tetracyclines and fluoroquinolones [16].
Prior to 2014, in the United Kingdom, seven cases of macrolide-resistant M. pneumoniae infections were reported between 2008 and 2011, one case in England and Wales and six cases in Scotland [1,2].This is the second report of macrolide-resistant M. pneumoniae strains detected in England and Wales, with one case previously documented for a single patient specimen from 2008 [1].Macrolide resistance in M. pneumoniae has been reported in Scotland at 19% (6/32) [2], considerably higher than the 9.3% documented here.This may reflect low sample numbers or sampling differences and it is important to note that the specimens examined for macrolide resistance in Scotland were from patients in whom macrolide resistance was considered most likely based on their clinical presentation or history, being one of the following: repeated specimen positive, remaining symptomatic following antibiotic treatment, admitted to critical care or having an underlying condition.
In this study a high number of samples were from a single city in England and a local epidemic cannot be excluded.There is no requirement for referral of M. pneumoniae-positive specimens to the reference laboratory in England and Wales.Systematic testing and referral of positive specimens does not occur.Therefore regional comparison was not possible.Nonetheless, the focus of this article was to highlight macrolide resistance rather than a specific regional cluster analysis.
Macrolides are currently recommended as the firstline treatment for M. pneumoniae infection in the UK [17].The 2011 British Thoracic Society guidelines for the management of community acquired pneumonia in children and adults suggest empirical macrolide treatment at any age if there is no response to first-line betalactam antibiotics or in the case of very severe disease [17,18].Tetracyclines (minocycline and doxycycline) and fluoroquinolones (levofloxacin and moxifloxacin) can be used to treat M. pneumoniae infections as an alternative to macrolides when clinically relevant [19], however, their use in children is limited due to effects on bone toxicity and cartilage development, respectively [20,21].
We did not isolate M. pneumoniae by culture from those specimens wherein M. pneumoniae was detected by PCR and therefore we were not able to confirm phenotypic macrolide resistance.However, point mutations within the 23SrRNA gene in clinical specimens and isolates, including the A2058G mutation, have previously been shown to confer resistance [16].Acquisition of resistance has been documented in patients receiving macrolides and resistance may develop as a consequence of antibiotic selective pressure [22].This is supported by the highest macrolide resistance rates being reported in countries with extensive macrolide use [15].Increased vigilance pertaining to macrolideresistant M. pneumoniae in the UK is recommended.LGV cases diagnosed in the UK.Duplicates were excluded and repeat diagnoses within 42 days (used to define a single episode of care across surveillance systems in England) were counted as a single episode [1].
Additional data, including sexual behaviour and clinical information, were collected through nationally coordinated enhanced surveillance of LGV in the UK between 2004 and 2010 [2].However, the most recent laboratory dataset lacks this enhanced information.We therefore matched laboratory reports for LGV diagnoses to the Genitourinary Medicine Clinic Activity Dataset (GUMCADv2), an anonymised patient-level electronic dataset, for all cases in England in 2014.All commissioned sexual health services in England have been mandated to return GUMCADv2 data, which include patient characteristics, other sexually transmitted infection (STI) diagnoses and services provided, since 2009 [3].A code for LGV diagnosis was introduced in 2011, such that most cases are now reported through GUMCADv2.
LGV diagnoses in female or heterosexual male patients in GUMCADv2 were excluded from this analysis because they may represent miscoding (six cases).

Background
LGV is a STI caused by the invasive L serovars of C. trachomatis.An outbreak among MSM was first reported in the Netherlands in 2003 and LGV outbreaks in MSM have since been reported by many high-income countries, with HIV co-infection being a common feature [4][5][6][7][8].Most reported infections are rectal, and the most common presentation is proctitis, associated with rectal pain, discharge and bleeding [5,9].Some cases of LGV, particularly in the beginning of the outbreak, were misdiagnosed as Crohn's disease [10,11].The complications of incorrectly treated or untreated LGV are serious, particularly for immunocompromised individuals, including genital ulcers, fistulas, rectal strictures and genital elephantiasis.
LGV acquisition is associated with concurrent STI infections and reported behaviours such as condomless anal intercourse, fisting and the use of sex toys [2].

Discussion
Since LGV: lymphogranuloma venereum.The strength of this study lies in the unique national dataset of laboratory confirmed LGV diagnoses, which we linked to clinical data for the most recent complete year.During the study period, LGV testing was only recommended for symptomatic patients and LGV contacts.However, a large multicentre case-finding study in the UK found that 27% of LGV infections were detected in patients without rectal symptoms, suggesting that infections might be missed [12,13].Patients might also be treated presumptively without LGV testing or never seek care, leading to further underestimation of LGV cases in the population.Other external factors might have influenced requests for LGV testing and the trends observed.These include the introduction of charging laboratories for LGV diagnostic testing (April 2014) and increased awareness of LGV among clinicians and microbiologists, which might have led to increased testing.We lack data on symptoms associated with LGV infection in this surveillance dataset.
The increase in LGV diagnoses coincides with upward trends in other STIs and sexually transmissible enteric infections among MSM, such as gonorrhoea, infectious syphilis, verotoxin-producing Escherichia coli and Shigella [14][15][16][17].Contributory factors might include sexual networks with high rates of partner change facilitated by social media networking sites and chemsex, and we know that HIV-positive MSM who engage in HIV sero-adaptive behaviours and have condomless sex with other HIV-positive men remain at particularly high risk [15][16][17].Our data suggest a need for a strengthened public health response to raise awareness of LGV among clinicians and patients.Social media might offer a means of rapid, low-cost dissemination of public health messages, with an additional benefit of facilitating user interaction [18].
There are also important implications for clinical management and microbiologists, including the need for robust partner notification, testing and treatment, and testing of HIV-positive MSM with asymptomatic C. trachomatis infection for LGV [19].
LGV treatment requires an extended course of antibiotics over non-LGV C. trachomatis, such that some patients may unnecessarily receive multiple courses of antibiotics; this risks introducing selection pressure for antimicrobial resistance [20].Clinicians should maintain a high index of suspicion for LGV in HIV-positive MSM with rectal symptoms, and consider treating presumptively for LGV according to national guidelines [21,22].Between October 2014 and March 2015, an estimated 66,000 cases of chikungunya virus infections were reported in French Polynesia, with an overall attack rate of 25% [1].At the same time, we observed an epidemiological cluster of cases Guillain-Barré syndrome (GBS), an acute and probably autoimmune demyelinating polyradiculoneuropathy that appears after a triggering (viral or bacterial) infection in almost two thirds of cases.GBS had already been associated with several arboviral diseases including chikungunya virus (CHIKV) infections [2,3], but a cluster as we reported here had never been described.

Cluster description
Among the reported chikungunya fever cases, ca 50 people developed complications (myocarditis, meningoencephalitis, GBS) and 18 died; most of them had comorbidities.Nine patients were admitted for GBS based on clinical assessment, in the French Polynesia tertiary hospital: three in November, three in December, two in January and one in February.Six patients were male (male/female ratio: 2), with a median age of 48 years (range: 37-77 years).Eight patients were Polynesian and one was Caucasian from Metropolitan France.Two patients had hypertension and one had hypertension and diabetes mellitus; the six others did not have any underlying conditions.
All nine were referred and then admitted to the department of neurology with a median length of stay of 11 days (range: 6-21 days).The patients were hospitalised within a median of eight days (range: 3-40 days) after the onset of symptoms of infection.Upon admission none had any symptoms of this acute phase which had presented as a dengue-like syndrome: all patients were febrile, eight had arthromyalgia, and three had a rash.GBS, presenting as a sensorimotor deficit beginning in the lower limbs and evolving to the upper limbs, was reported for eight patients; the last patient only had facial diplegia with sensory disorders of the face.Seven patients presented with signs of cranial nerve involvement, facial paralysis, dysphonia, dysarthria or dysphagia, associated with severity of GBS [4].Among them, four were hospitalised in the intensive care unit for a median length of stay of six days (range: 2-15 days).

Diagnostic findings in Guillain-Barré syndrome patients
Eight patients had IgM and IgG antibodies against CHIKV and one was positive for CHIKV in RT-PCR positive.Serological evidence of past dengue or Zika virus infection (IgG) was found in nine and eight patients, respectively, IgM for both infections was negative in all cases; no PCR was done for Zika virus.No PCR was performed for dengue virus either but when performed, it was negative.
Brain and spinal magnetic resonance imaging (MRI) was performed in seven patients within a median of nine days (range: 5-15 days) after the onset of neurological symptoms.Among the seven patients presenting with cranial nerves involvement, MRI showed signs of neuritis of the facial nerves in two patients and neuritis of the facial and left trigeminal nerves in one patient; no abnormalities were seen in the others.MRIs which disclosed signs of neuritis were performed at least eight days after the beginning of GBS; those whose MRI was normal had it at day 5 and day 6; two patients only had a computerised tomography brain scan without contrast enhancement.
Electromyography was performed in all nine patients within a median of seven days (range: 3-14 days) after the start of GBS.It disclosed significant prolongation of the motor distal latencies with reduction of distal motor amplitudes, which attested a severe and predominant impairment of motor conduction in distal part of the nerves; motor conduction of more proximal nerve segments was less affected and little sensory impairment was seen.
All patients underwent a lumbar puncture, which was performed within a median of six days after the onset of neurological deficit (range: 2-15 days).Cerebrospinal fluid (CSF) was characterised by an albuminocytologic dissociation (elevated total protein concentration without CSF cell count abnormality) in all cases; median spinal protein concentration was 1.26 g/L (range: 0.82-4.97;norm <0.5), whereas the median cell count was 2/mm 3 (range: 1-6; norm <5).Glucose levels were normal, with a median CSF/plasma ratio of 0.6 (range: 0.43-0.70;norm <0.75); CSF lactate levels were slightly elevated at a median of 167 mg/L (range: 117-251; norm <190).Plasma level of antiganglioside antibodies was measured in eight patients (anti-GM1, GM2, GD1a, GD1b, anti GQ1b IgM and IgG antibodies); a low positivity of anti-GM2 was noted in one case and of anti-GD1a in another case.
All patients were treated with intravenous immunoglobulin.Six patients were discharged to a functional rehabilitation centre for a median stay of 28 days (range: 19-60 days).In all patients, electrophysiological parameters quickly returned to almost normal levels within less than three months.

Discussion
Chikungunya fever is an arboviral disease that usually manifests as a self-liming dengue-like syndrome with high fever, severe arthralgias and myalgias, and a maculopapular rash.Rare but severe complications may occur, such as myocarditis, hepatitis and neurological manifestations [5].
Neurological tropism of CHIKV seems to be lower than of other arboviruses such as dengue, West Nile or yellow fever viruses, but several studies have described, especially during epidemics, neurological manifestations such as meningoencephalitis, seizures or GBS [6].In some cases, IgM antibodies against CHIKV have been found in CSF of patients with meningitis, supporting the theory of neuroinvasion [7].
While the annual incidence of GBS in French Polynesia is between 1 and 2 per 100,000 inhabitants, nine cases of GBS were admitted to our hospital during this sixmonth outbreak of chikungunya, a four-to nine-fold increased incidence, leading us to suspect a causal relationship between CHIKV infection and GBS.To our knowledge, this is the first series of GBS temporally associated with a chikungunya fever outbreak.Characteristics of the neurological presentation of our patients are not different from GBS related with, or following other aetiologies.We thus recommend keeping in mind that GBS is not an uncommon possibility in neurological disorders associated with CHIKV virus infection, especially in an epidemic context.Finally, it is interesting to note that this is the second arbovirustriggered outbreak of GBS in French Polynesia within two years: the first one, during the Zika fever outbreak from 2013 to 2014, resulted in 42 cases and a 20-fold increase in the annual incidence of GBS [8].
Our report adds to the mounting body of evidence about the possibility of severe neurological disease following CHIKV infections.
Ebola virus can persist in semen after recovery, potentially for months, which may impact the duration of enhanced surveillance required after interruption of transmission.We combined recent data on viral RNA persistence with weekly disease incidence to estimate the current number of semen-positive men in affected West African countries.We find the number is low, and since few reported sexual transmission events have occurred, the future risk is also likely low, although sexual health promotion remains critical.
In this study, a negative binomial distribution is fitted to recent data on persistence of Ebola virus (EBOV) RNA in semen after Ebola virus disease (EVD) symptom onset in EVD survivors.Given the prior reported incidence of EVD in each affected region of Guinea, Liberia, and Sierra Leone, the fitted distribution is used to estimate and model the number of men in these countries with EBOV RNA present in semen, in each week since mid-2014.According to this, the total number of EBOV RNA semen-positive individuals in January 2016 would be low (n=73; 95% confidence interval (CI): 15-331).Since few reported sexual transmission events have been documented [1], the future risk of such transmission is also likely low.

Modelling Ebola virus RNA persistence in semen
EBOV can persist in immunoprivileged sites within the body after recovery from infection, specifically in semen [1,2].Post-recovery sexual transmission (PRST) of EBOV via semen has been documented in the ongoing West African outbreak [3].Understanding potential EBOV shedding after recovery is critical to determining duration of surveillance of survivors, and may impact the length of enhanced surveillance following the interruption of transmission in a country; which currently begins 42 days after the final case and lasts 90 days [4].Sierra Leone is currently the only country in West Africa in the enhanced surveillance period, which began on 7 November 2015.
In a separate study, ninety three men had one semen test two to 10 months after onset of confirmed EVD symptoms [1].Samples were tested by reverse transcription-polymerase chain reaction (RT-PCR) for the presence of EBOV RNA.A positive test by RT-PCR means that viral RNA is present, but does not necessarily mean that infectious virus is present in the sample.The number of positive, negative, or indeterminate samples was reported by month since onset of EVD symptoms and we took the number of days to be the mid-point of each month (Table 1).
We estimated the probability that semen was no longer RNA positive by the sampling time, where indeterminate samples were treated as negative.We fitted a negative binomial distribution for the semen clearance time, by maximum likelihood (Figure 1).We extrapolate to 85 weeks after symptom onset.

Estimating numbers of men with Ebola virus RNA in semen in West Africa
The fitted distribution was used to calculate the number of men with semen positive for EBOV RNA present each week, given the prior incidence of EVD in each affected region of Guinea, Liberia, and Sierra Leone.
For each area (prefecture, county or district) in Guinea, Liberia and Sierra Leone, we use confirmed and probable cases available from the World Health Organization (WHO).The WHO patient database, which is curated and more accurate than the situation reports but subject to delay, was used except for recent weeks where we switch to the WHO situation reports (1 January 2014 to 11 October 2015) because counts were more up to date [5].Except for the Western Area Districts, Sierra Leone (switch date: 3 May 2015; data not shown), the switch date between WHO data sources was defined within the six weeks prior to the publication date of the last week reported (14 October 2015), as the earliest week when the number of cases in the situation report exceeded that in the WHO patient database.
We assume 60% case fatality for all weeks, and that 40% of survivors are male adults [6].

Sensitivity of model of RNA persistence in semen to chosen distribution
Due to the low number of samples, and the lack of samples at long time periods, we are unable to determine which parametric distribution fits best (Figure 3).Results above are presented for the negative binomial distribution, and here we examine the sensitivity of our estimates to the chosen distribution.We show the fit to the data (Figure 3A), probability distribution of duration of semen RNA positivity (Figure 3B), and the number of EBOV RNA semen-positive individuals in the first week of January 2015, the week ending 8 November 2015 and the first week of January 2016 for Guinea (Table 2), Liberia (Table 3) and Sierra Leone (Table 4).
In all tested distributions the values for the number of individuals in January 2015 are comparable, as are estimates on 8 November 2015.In estimates for January 2016, the effect of the difference in the tail of the distributions becomes clearer.

Sensitivity to underreporting of estimations of numbers of men with Ebola virus RNA-positive semen
We tested the sensitivity of our estimates to the assumed fraction of EVD cases that are reported.We show estimates for complete (or 100% reporting) (as above), constant 70% reporting, or a rising reporting fraction, beginning at 30% early in of the epidemic (1 January 2014), reaching 95% near the end of the epidemic (11 October 2015) (Figure 4).Table 5 shows the estimated number in week ending 8 November 2015, which is marked in Figure 4 as a grey line.
Although there are differences between the curves, by November 2015, the vast majority of surviving men would no longer be EBOV RNA semen-positive.Indeed, the number of men remaining is fairly small irrespective of underreporting.EBOV: Ebola virus.
The maximum duration of EBOV RNA semen positivity is currently unknown, and in our analysis the inferred maximum duration is sensitive to the shape of the decay distribution chosen to fit the available data.The mean number of EBOV RNA semen-positive men at each time point is less sensitive to the choice of distribution, although the confidence intervals vary widely on this assumption.

Discussion
Our analysis indicates that the number of men remaining in West Africa with EBOV RNA detectable in their semen is currently low and continuing to fall.The geographical distribution of these individuals is heterogeneous, and is related to past incidence levels and the timing of cases in those districts.
To better understand the risk of onward transmission, the relationship between testing positive for EBOV RNA by RT-PCR, and the of sexual transmission needs quantification.Recent sexual transmission events [3] further highlight the urgent need for comprehensive survivor screening programmes, which include testing of bodily fluids such as semen to determine a more certain time at which RNA is no longer present.Such programmes would not only provide insight into how to protect the intimate contacts of survivors, but can provide reassurance to the many survivors who are likely no longer EBOV semen-positive.
Our base-case estimates do not include suspected cases, underreporting of symptomatic cases or the possibility of EBOV RNA-positive semen in asymptomatic cases.Under these circumstances, the number of EBOV RNA semen-positive individuals is slightly increased (Figure 4).In addition, although we present point estimates for numbers of remaining EBOV RNA semen-positive survivors, the values rely not only on accurate EVD incidence data, but also on assumptions of constant survival rates, as well as statistical uncertainty in the fitting procedure.Therefore, point estimates should be interpreted with care, and attention given to the wide confidence intervals.
Up to 20 suspected PRST events have been reported in West Africa to date [1], although ring vaccination of at-risk contacts in Guinea may have reduced late transmission [7].Even assuming 20 PRST events to be a substantial underestimate, future numbers may be low.Given this low potential for transmission, we should be cautious not to further stigmatise an already marginalised group.However, since a single PRST event could restart wider transmission, and the duration for which men may remain EBOV semen-positive is long, continued promotion of sexual health and EVD surveillance remain vital.

Table 4
Comparison of predicted numbers of Ebola virus RNA semen-positive survivors in Sierra Leone on three dates according to the fitted distribution selected

Introduction
Acute gastroenteritis is one of the commonest paediatric presenting complaints with the predominant cause being rotavirus (RV).Almost all children will have suffered from RV gastroenteritis by the time they are five years old.Worldwide, RV is estimated to be responsible for more than 450,000 deaths in children every year [1] although with good nutritional status and access to medical care, death due to RV infection is exceptionally rare.In Bristol, as in the whole of the United Kingdom (UK), it is a highly seasonal infection occurring in annual epidemics in the late winter and early spring, although in tropical regions it persists year-round [2].RV is a highly infectious organism, able to spread even in countries with high standards of hygiene.The only effective control strategy is vaccination [3].The World Health Organization has recommended that all countries should include a vaccine against RV in their childhood schedules [4].As of March 2015, only 12 of the 75 countries to have introduced RV vaccination into their primary infant schedules were in Europe [5].
A 2007 health economic analysis estimated that if the vaccine could be purchased for a favourable price, RV vaccination could be cost-effective in the UK [6,7].
Although the UK has been at the forefront of universal childhood programmes using meningococcus group C conjugate and more recently live attenuated influenza vaccines, vaccination against a disease that is extremely common but rarely leads to death or longterm morbidity required a different paradigm and it was not until July 2013 that RV immunisation was introduced into the routine childhood vaccine schedule at two and three months of age [8].With an upper age limit of 24 weeks placed on the last dose of vaccine due to the reported association with intussusception, a catch-up campaign was not possible.It is now important to evaluate the impact of this measure on the burden of children's illness and to evaluate whether the £20 (€28) million annual healthcare saving predicted by the Department of Health will be realised [9].As not all patients were able to provide a stool sample, the proportion of all gastroenteritis attendances and admissions that were caused by rotavirus was estimated from the proportion of samples received over the same time period that were confirmed to be rotavirus positive.Similarly, the proportion of positive results from stool samples received from children of different ages was used to estimate the overall age distribution of rotavirus cases.

Methods
Our strict hospital infection control policy meant that any patient who developed gastroenteritis while admitted was tested for viral causes.By linking all positive stool results from our laboratory to admission date  and diagnosis, any later samples from admitted gastroenteritis patients could be included and patients admitted with a non-gastroenteritis diagnosis who tested positive for RV more than 48 hours after their admission could be retrospectively identified as nosocomial infection.By definition these patients were not included in the analysis of the attendance or admitted cohorts.
In the UK, hospitals are paid according to an annually negotiated tariff based on the coded discharge diagnoses for an episode of care.From the 2013/2014 National Health Service tariffs [11] the cost of an emergency department attendance (VB09Z) was £96 (€135), and short-term viral gastroenteritis admission (PA21B) was £504 (€707).We used these to estimate the costs saved by the health service through RV vaccination.
Data were recorded in Microsoft Access.Data cleaning and statistical analysis was done using R [12].Significance of annual changes in rates of attendance and admission were assessed using negative binomial regression model using year as a cofactor.Mann-Whitney U test was used to compare age distributions and chi-squared test for proportions.
As this project involved analysis of the results of non-invasive standard clinical investigation and anonymised routine clinical data, this work was assessed as being a service evaluation by University Hospitals Bristol NHS Foundation Trust, with no ethical review or informed consent for research required.

All cause gastroenteritis
In total, during the three rotavirus seasons there were 3,410 emergency department attendances with median age 18 months (interquartile range (IQR): 9-42; range: 0-202) and 722 admissions with median age 17 months (IQR: 9-43; range: 0-202).Between 2012 and 2013 there was significant variation in the number of all-cause gastroenteritis attendances (p < 0.001) but not in the proportion admitted (p = 0.7).In 2014 there was a 48% reduction in attendances (p < 0.001) and a 53% reduction in admissions (p < 0.001) compared with the mean in the pre-vaccine years 2012 and 2013.
There was a 67-71% (p < 0.001) reduction in the total number of bed days occupied: equating to 1.7-2 fewer occupied beds in the hospital every day during the six-month period examined (Table 1).Median age of attendance rose significantly in the winter following vaccine introduction (Table 2) (p < 0.05).There was no significant difference in length of admission.
Figure 1 compares the fortnightly total numbers of attendances to the emergency department with gastroenteritis symptoms, demonstrating the onset of the gastroenteritis season for the three years of the study.Pre-vaccine rates of gastroenteritis attendance peaked in week 7 of 2012 and week 15 of 2013, while in 2014 the seasonal epidemic was attenuated with a possible peak between weeks 8 to 10. Figure 2 demonstrates the corresponding number of patients admitted with gastroenteritis per fortnight during the study.
The age distributions of cases for the three years show that after vaccine introduction there were reductions in number of attendances 3) and admissions (Figure 4) across all age groups and not just in the infants under the age of one that would have been eligible for the vaccine.

Rotavirus gastroenteritis
During the surveillance period samples were obtained from 35%, 30% and 30% of gastroenteritis attendances with diarrhoea in the three respective seasons.In 2012 and 2013, 54% and 65% of these were positive for RV; in 2014 this proportion fell to 36% (p < 0.001) (Table 3). the age distributions of positive samples and the overall gastroenteritis attendance rates (Figure 1) reveals that as well as a 94% drop in RV attendances among those less than 12 months of age, there was also a 67-70% reduction in those too old to have been vaccinated (1-4 years).
In children who were admitted with gastroenteritis, the proportions of RV positive samples per year were 59%, 63% and 40%, respectively.The number of gastroenteritis admissions likely to be attributable to RV fell from 175 in 2012 and 180 in 2013 to 55 in 2014: a 69% reduction (p < 0.001).
We identified six cases of nosocomial RV transmission in 2014 compared with eight in 2012 and 15 in 2013 (p = 0.16).

Financial effects
Between the years 2012 and 2013 we calculated RV to be responsible for a mean of 14.5 ED attendances and 3.3 admissions per 1,000 children under the age of five.
In 2014 this fell to 4.6 attendances and 1 admission per children under five years of age.If this fall is due to RV vaccine use, extrapolating these findings to the national paediatric population under the age of five years [13] would equate to approximate first year reductions of 35,700 ED attendances and 8,120 admissions.Before one whole birth cohort had been protected, we calculate secondary care savings of ca £7.5 (€10.5) million in the first year of implementation.

Discussion
This is the first report of RV vaccine impact in the UK.This early evidence points to direct as well as possible indirect effects of this new immunisation programme   the first seasonal epidemic, the first seven weeks of data were collected retrospectively.
As can be seen from the differences between 2012 and 2013, RV epidemics vary in size between years even in the absence of immunisation.It has recently been reported that 2014 was an exceptionally low RV year in both France and the Netherlands [18], despite neither country routinely using a RV vaccine.Although it is possible that the UK's 2014 epidemic was also unusually small coincidentally to the commencement of vaccination, we feel it is unlikely that the entire effect observed effect is due to this.Case-control studies have shown that both licensed RV vaccines provide excellent direct protection in industrialised countries [19,20] with evidence of herd protection [21].Mathematical models predict that after the introduction of RV vaccine there will be an increased average age of cases and a delay in the seasonal peak [22] [23].
With widespread vaccination removing the majority of susceptible patients, a 'honeymoon period' of very low disease incidence shortly after the introduction is also expected.But with the gradual accumulation of an unvaccinated naive fraction, at some point there may be a rebound rise in cases.Key variables that determine the timing of this phenomenon include vaccine uptake and consistency in coverage over time and place, duration of vaccine-induced protection, and the transmissibility of the infection.The reduced number of cases seen in children too old to have been vaccinated is unexpected; it is not possible to discern whether this is evidence of herd effect or represents the true size of the underlying 2014 UK seasonal epidemic.For reasons unknown, rotavirus epidemiology appears to have changed abruptly in the Netherlands, but in the absence of clinical disease (or vaccination), susceptible patients will continue to accumulate creating a population susceptible to future outbreaks.To date this has not been reported in 2015 [24].
The United States (US) introduced a pentavalent RV vaccine (RotaTeq-SMSD) in 2006 and, with 50-60% vaccine coverage, a dramatic reduction in cases was observed the following season [25].After a resurgence of disease in year two, cases have subsequently oscillated in number biennially, cycling between 60% and 80% lower than the pre-vaccine baseline [26].These dynamics may be due to the suboptimal vaccine uptake, which in 2013 was still only 72.6%, 10% lower than other primary vaccines [27].In 2006, Belgium was the first European country to introduce the same vaccine as the UK (Rotarix) and rapidly achieved vaccination coverage > 90% [19].To date only three years' post-introduction data have been published, with no rebound yet reported [28].Public Health England have reported UK RV vaccine coverage rates of 93% first dose and 88% complete course and a 67% reduction in RV laboratory reports compared with a ten year average [29].Our local RV vaccination rates were similar, 91% first dose and 86% completed course.With a different vaccine at higher coverage rates than the US, the UK's eventual epidemiology is likely to be more similar to Belgium.Ongoing surveillance will be important not only to track any rebound but also because the monovalent vaccine (Rotarix) has relatively lower efficacy against non G1 strains of virus [30,31] and may result in their relative emergence as overall RV circulation declines.However natural year-to-year genotype fluctuations make interpretation of such ecology challenging.After Brazil introduced the monovalent vaccine, a three year progressive rise in G2P4 (89,93,100%) was followed by a sudden return of G1P8 (68%) in 2009, with non-vaccine genotypes predominating subsequently on a background of sustained public health benefits with significant reductions in gastroenteritis attendances, admissions and deaths [32].
The UK health economic analysis [33] estimated that RV was responsible for 9.3 emergency department consultations and 4.5 admissions per 1,000 children under the age of five years and predicted secondary care savings of £7.4 (€10.4) million with the use of RV vaccine, almost exactly the same as our findings.The impact on primary care is not yet known, but any reduction in the estimated 100,000-150,000 annual consultations due to RV [33] will have had wider benefits by allowing others to access pressured services.However, while the prevention of healthcare utilisation is important, the additional benefits of this vaccine to society at large may have been much greater by sparing children an unpleasant disease, sparing families time missed from productive work while caring for them and by preventing associated secondary cases.
Just one season after vaccine introduction, it is too early to conclude that our data entirely reflect vaccine effectiveness rather than epidemiological happenstance.But they provide a first description of remarkable trends which will need to be followed closely over the seasons to come.
On 24 November 2015, the evidence-based '2015 European guideline on the management of Chlamydia trachomatis infections' was published online [1].This guideline is a comprehensively updated version of the 2010 European C. trachomatis guideline [2] and provides up-to-date and detailed guidance regarding the testing, diagnosis, treatment and general management of C. trachomatis infections in Europe.The important updates include, for example: • broader indications for testing and treatment of C. trachomatis infections; • clearer recommendation of using exclusively validated and quality assured highly sensitive and specific nucleic acid amplification tests for diagnosis; • advice on (repeated) C. trachomatis testing; • recommendations of increased testing particularly at sexually transmitted infections and sexual health clinics to reduce the incidence of pelvic inflammatory disease and prevent exposure to infection; • recommendations to identify, verify and report C. trachomatis variants.
Details are also available in the newly launched guideline regarding the aetiology, transmission, clearance, epidemiology and taxonomy of C. trachomatis, clinical features, recommended diagnostics (including quality assurance), advice for C. trachomatis infected patients, indications for therapy, recommended and alternative treatment regimens for urogenital and extragenital C. trachomatis infections, contact tracing and management, and the notification of C. trachomatis cases [1].
For further details regarding background, evidence base of recommendations and discussions, see also the published background review for the guideline [3].
C. trachomatis infection, which most frequently is asymptomatic, is the most common bacterial sexually transmitted infection and a major public health concern globally.In 2012, the World Health Organization (WHO) estimated 130.9 million urogenital cases among adults worldwide (8.9 million in the WHO European region) [4].In the European Union (EU) and European Economic Area (EEA), 384,555 chlamydial cases were reported in 26/31 EU/EEA Member States (incidence: 182 cases per 100,000 population) in 2013.The incidence was higher among females (incidence: 207) than in males (incidence: 153) [5].The true incidence is certainly significantly higher, due to the asymptomatic nature of chlamydial infection, lack of sufficient testing, appropriate diagnostic methods and surveillance systems across Europe.For example, 83% of all cases were reported in four countries (Denmark, Norway, Sweden and the UK).Two thirds of all chlamydial infections were reported in the 15-24 years age group, with the highest incidence among females 20 to 24 years of age (incidence: 1,717).Heterosexual transmission accounted for 88% of cases.In countries reporting consistently between 2004 and 2013, the overall reporting rate has increased by 68%.

Figure 2
Figure 2Cases of shigellosis in refugees and two Austrian residents, by location of detection, Austria, 18 July to 18 November 2015 (n=23)

Figure 1
Figure 1Fit of a negative binomial distribution to published data on detection of Ebola virus RNA in semen samples

Figure 3
Figure 3Comparison of distributions that can be used to fit the available data on proportions of Ebola virus survivors with semen positive for Ebola virus RNA

Figure 4
Figure 4Effect of underreporting of true Ebola virus disease cases on the number of men with semen positive for Ebola virus RNA in Guinea, Liberia and Sierra Leone

Figure 1
Figure 1Distribution of all-cause gastroenteritis attendances, fortnightly totals, Bristol Royal Hospital for Children, United Kingdom, 2012-2014

Figure 2
Figure 2Distribution of all-cause gastroenteritis admissions, fortnightly totals, Bristol Royal Hospital for Children, United Kingdom, 2012-2014

Figure 3
Figure 3Age distribution of all-cause gastroenteritis attendances < 18 years of age, Bristol Royal Hospital for Children, United Kingdom, 2012-2014 July to 18 November 2015 (N=23)

Table
Cases of shigellosis in refugees and Austrian residents, working at two transit centres, by age, date, province and location detected, country of origin, Shigella species and resistance, Austria, 18 July to 18 November 2015 (N=23) NA: not available; Neg: negative; Pos: positive; RC: reception centre; TC: transit centre.

Table Details
of patients with macrolide-resistant Mycoplasma pneumoniae-positive clinical specimens, England and Wales, September 2014-September 2015 (n=4) United Kingdom (UK) national data show a sharp increase in diagnoses of lymphogranuloma venereum (LGV) since 2012.Most cases are in men who have sex with men (MSM) living in London, with high rates of co-infection with HIV and other sexually transmitted infections.In light of these data, and the recent finding that one quarter of LGV infections may be asymptomatic, clinicians should be vigilant in testing for LGV, including in asymptomatic HIV-positive MSM.Laboratory diagnoses of lymphogranuloma venereum (LGV) in the United Kingdom (UK) declined between 2010 and 2012, but the most recent data show near doubling of cases since 2012 to unprecedented levels in 2014 (679 cases).This trend has continued into 2015, with 683 cases diagnosed by 30 September.In 2014, most cases were in men who have sex with men (MSM) and around three quarters were HIV-positive.Here we report national surveillance data showing trends in LGV diagnoses in the UK from 2003 to September 2015.Testing protocol and data sourcesRectal, genital or urine samples from patients with symptoms compatible with LGV and diagnosed with Chlamydia trachomatis in England, Wales and Northern Ireland, and their sexual contacts with C. trachomatis, are submitted by local laboratories for LGV typing to the Public Health England national reference laboratory, the Sexually Transmitted Bacteria Reference Unit (STBRU) in London.Scottish samples from symptomatic patients are similarly submitted to the Scottish Bacterial Sexually Transmitted Infections Reference Laboratory (SBSTIRL) in Edinburgh.In addition, since 2007, samples from asymptomatic HIV-positive MSM diagnosed with C. trachomatis are also sent to SBSTIRL.During the reporting period, (January 2003 to September 2015) STBRU and SBSTIRL diagnoses accounted for all confirmed

Table 1
Number of initial samples tested and time since Ebola virus disease onset 93 samples tested and reported in Deen et al. 2015[1].We use the midpoint of the month of testing as number of days.

Table 2
Comparison of predicted number of Ebola virus RNA semen-positive survivors in Guinea on three dates according to the fitted distribution selected

Table 3
Comparison of predicted number of Ebola virus RNA semen-positive survivors in Liberia on three dates according to the fitted distribution selected CI: confidence interval.Mean, lower and upper 95% CIs from 5,000 bootstrap samples are given.

Table 5
Estimated number of men with Ebola virus positive semen in Guinea, Liberia and Sierra Leone, as of 8 November 2015 stratified by the value of underreporting assumed in the data

Table 1
Number of cases of all-cause gastroenteritis aged < 18 years seen, Bristol Royal Hospital for Children, United Kingdom, January-July 2012-2014 (n=3,409)

Table 2
Comparing age at attendance or admission and length of admission for all-cause gastroenteritis < 18 years, Bristol Royal Hospital for Children, UnitedKingdom, 2012Kingdom,  -2014 (n=3,409)    (n=3,409) IQR: interquartile range.p values describe significance of differences in comparison to 2014.

Table 3
Number of rotavirus positive samples and percentage testing positive by month in children < age of 18 years, Bristol Royal Hospital for Children, 2012-2014 (n=677)