Importance of whole genome sequencing for the assessment of outbreaks in diagnostic laboratories: analysis of a case series of invasive Streptococcus pyogenes infections.

Outbreaks of Streptococcus pyogenes hypervirulent clones are constant public health threats. In western Switzerland, an increase of severe cases of S. pyogenes invasive infections was observed between December 2015 and March 2016. Our aim was (i) to investigate these cases by the use of Whole Genome Sequencing (WGS) and (ii) to determine the specific virulome and resistome of each isolate in order to undertake adequate public health measures. Eleven Streptococcus pyogenes strains isolated from 11 patients with severe invasive infections between December 13, 2015 and March 12, 2016 were included in our study. Practically, emm-typing, MLST and WGS were used to investigate the relatedness between the isolates. The presence of virulence and antibiotic resistance genes as well as mutations in transcriptional regulators of virulence and in genes encoding for antibiotic targets were assessed. Three and two groups of isolates shared the same emm-type and ST type, respectively. Single Nucleotide Polymorphism (SNP) analysis revealed 14 to 32 SNPs between the strains of the same emm-type group, ruling out the possibility of a clonal outbreak. Mutations found in covS and rocA could partially explain an increased virulence. As these reassuring results were obtained in less than 10 days, no specific hospital hygiene and no dedicated public health measures had to be undertaken. WGS is a powerful technique to discriminate between closely related strains, excluding an outbreak in less than 10 days. Moreover, WGS provided extensive data on the virulome and resistome of all these strains.

[Leptospirosis in a family after whitewater rafting in Thailand]. / Leptospirose famitiate apres rafting en Thaïlande.

Leptospirosis is a zoonosis found worldwide, with an incidence that is approximately 10 times higher in the tropics than in temperate regions. The main reservoir of leptospirosis is the rat and human infection usually results from exposure to infected animal urine or tissues. Only 10% of cases are symptomatic. We present here two confirmed and two probable cases of leptospirosis in a family returning from whitewater rafting in Thailand, illustrating the wide variety of the clinical manifestations of this infection. Two of the patients were hospitalized and presented a probable Jarisch-Herxheimer reaction after initiation of beta-lactam therapy. The two others patients were treated empirically with doxycycline. We discuss here some relevant aspects of the epidemiology, clinical manifestations, therapy and the challenge of an early diagnosis of leptospirosis.

[Infections transmitted from cats and dogs]. / Infections transmises par les chats et les chiens.

The risk of zoonose transmitted from cats and dogs has increased as these animals have been more and more included in family life to become real household members. This paper reviews the main bacterial, parasitic, viral and fungal infections that could be transmitted to humans by these pet animals in different situations. Although the risk of human disease is relatively low for most of the presented infections, its recognition is important to prevent some exposures, to apply correct prophylactic measures after bites, and to include these zoonoses in the differential diagnosis in case of illnesses that could have an infectious origin, particularly in immunocompromised patients.

Influence of environmental temperature and heatwaves on surgical site infection after hip and knee arthroplasty: a nationwide study.

BACKGROUND: Previous studies reported higher incidence of surgical site infection (SSI) after procedures performed in summer or with high temperatures. However, no study used detailed climate data to assess this risk after hip and knee arthroplasty, and no study specifically investigated the role of heatwaves. AIM: To assess the impact of higher environmental temperatures and heatwaves on SSI rates after hip and knee arthroplasty. METHODS: Data on hip and knee arthroplasty procedures performed between January 2013 and September 2019 in hospitals participating in the Swiss SSI surveillance were linked to climate data extracted from weather stations located in their vicinity. The association between temperature, heatwaves and SSI was studied using mixed effects logistic regression models fitted at the patient level. Poisson mixed models were fitted for both calendar year and month of the year to investigate the SSI incidence trajectory over time. RESULTS: We included 116,981 procedures performed in 122 hospitals. Significantly higher SSI rates were observed for procedures performed in the summertime (incidence rate ratio 1.39, 95% CI (1.20-1.60), P<0.001; reference: autumn) or in calendar months in which the mean temperature was above 20 °C (reference 5-10 °C; odds ratio 1.59, 95% CI (1.27, 1.98), P<0.001). We observed a slight but non-significant increase in the rate of SSI during heatwaves (1.44% versus 1.01%, P=0.2). CONCLUSION: SSI rates after hip and knee replacement appear to increase with higher environmental temperature. To establish whether, and to what extent, heatwaves increase the risk of SSI, studies involving geographical areas with larger variability in temperature are needed.

Scoring system to predict the risk of surgical-site infection after colorectal resection.

BACKGROUND: There is no dedicated scoring system for predicting the risk of surgical-site infection (SSI) after resection of the colon or rectum. Generic scores, such as the National Nosocomial Infections Surveillance index, are not used by colorectal surgeons. METHODS: Multivariable analysis of risk factors for SSI was performed in patients who underwent resection of the colon or rectum, and were followed during the first month after operation. A logistic regression model was used to identify determinant variables and construct a predictive score. RESULTS: There were 534 patients of whom 114 (21·3 per cent) developed SSI. In multivariable analysis, four parameters correlated with an increased risk of SSI: obesity (odds ratio (OR) 2·93, 95 per cent confidence interval 1·71 to 5·03), contamination class 3-4 (OR 3·33, 2·08 to 5·32), American Society of Anesthesiologists grade III-IV (OR 1·82, 1·14 to 2·90) and open surgery (OR 2·22, 1·01 to 4·88). Each of these contributed 1 point to the risk score. The observed risk of SSI was 5 per cent for a score of 0, 12·0 per cent for a score of 1 point, 18·7 per cent for 2 points, 44 per cent for 3 points and 68 per cent for 4 points. The area under the receiver operating characteristic curve for the score was 0·729. CONCLUSION: A simple clinical score based on four preoperative variables was clinically useful in predicting the risk of SSI in patients undergoing colorectal surgery.

[The changing epidemiology of sexually transmitted infections in Switzerland]. / Infections sexuellement transmissibles en Suisse: un paysage en transformation.

Sexually transmitted infections (STI), such as syphilis, gonorrhoea and infections caused by Chlamydia have been increasingly reported in Switzerland during the last decade. After having consistently decreased since the early 90s, reports of HIV infections were on the rise from 2000 to 2008. STIs are thus far from being controlled in Switzerland and their epidemiology has become more complex: different STIs circulate in different populations. The national program for HIV and STI 2011-2017 (PVNI) takes this challenge up and covers now the prevention, screening and treatment of all STIs. Primary care physicians, gynaecologists and specialists have an important role to play in provider initiated testing and counselling (PICT) and in the treatment of STIs.

[Neurotoxic effects of antimicrobial agents]. / Neurotoxicité des anti-infectieux.

Antimicrobial agents are occasionally responsible for significant neurological toxicity, the incidence of which is difficult to determine due to numerous confounding factors. It is nonetheless crucial to include this possibility in the differential diagnosis of any new or worsening neurological condition happening during antimicrobial treatment. Except for well described side effects (aminoglycoside ototoxicity) it is a rule out diagnosis and often necessitates a thorough metabolic and neurological work up. Once the diagnosis is strongly suspected, the therapeutic approach should always include the discontinuation of the offending agent, supportive measures and occasionally specific treatment. This article describes the wide possible neurological presentations and includes summary tables according to antimicrobial class.

[Resistant enterobacteria: explosion of extended-spectrum beta-lactamases]. / Entérobactéries résistantes: explosion des beta-lactamases à spectre élargi.

During the past recent years, Enterobacteriaceae have supplanted Gram-positives in terms of frequent resistant bacteria seen in the outpatent setting. This change involves common opportunistic pathogens such as E. coli and K. pneumoniae. It is mainly due to the appearance and dissemination of extended-spectrum beta-lactamases (ESBL), that hydrolyse penicillins and cephalosporins. Bacteria producing these enzymes are often also resistant to quinolones and trimethoprime-sulfamethoxazole. This article, illustrated by a clinical case, presents the current epidemiology of ESBL-producing Enterobacteriaceae and the possible prevention measures and treatment options to fight the growing number of infections that they are causing.

Nosocomial influenza in south-western Swiss hospitals during two seasonal epidemics: an observational study.

BACKGROUND: In Switzerland each year, influenza leads to between 112,000 and 275,000 medical consultations. Data on nosocomial influenza infection are limited. AIM: To describe nosocomial cases of seasonal influenza in south-western Switzerland. METHODS: This study was conducted during two seasonal influenza epidemics from 2016 to 2018 in 27 acute care public hospitals in south-western Switzerland. During these two time-periods, every patient hospitalized for >72 h who was positively screened by reverse transcription-polymerase chain reaction or antigen detection for influenza was included in the survey. Characteristics of patients included age, sex, and comorbidities. Included patients were followed up until discharge or death. Complications and administration of antineuraminidases and/or antibiotics were registered. FINDINGS: The median influenza vaccine coverage of healthcare workers was 40%. In all, 836 patients were included (98% with type A influenza virus in 2016-2017; 77% with type B virus in 2017-2018). Most patients (81%) had an unknown vaccine status. Overall, the incidence of nosocomial influenza was 0.5 per 100 admissions (0.35 per 1000 patient-days). The most frequent comorbidities were diabetes (20%), chronic respiratory diseases (19%), and malnutrition (17%). Fever (77%) and cough (66%) were the most frequent symptoms. Seventy-one percent of patients received antineuraminidases, 28% received antibiotics. Infectious complications such as pneumonia were reported in 9%. Overall, the all-cause mortality was 6%. CONCLUSION: The occurrence of nosocomial influenza underlines the importance of vaccinating patients and healthcare workers, rapidly recognizing community- or hospital-acquired cases, and applying adequate additional measures to prevent dissemination, including the timely administration of antineuraminidases to avoid antibiotic use (and misuse).

[What is the optimal duration of antibiotics in common infections?]. / Quelle est la durée optimale de l'antibiothérapie pour les infections fréquentes?

Defining the optimal duration of antibiotic treatments is crucial to reduce toxicity and the emergence of resistance. Community acquired pneumonia can be treated in 5 days when the clinical response is rapidly favorable, as determined by simple clinical criterias. Acute cystitis can be treated by a 5-day course of nitrofurantoïne, or 3 days of trimethoprim-sulfaméthoxazole, saving the use of quinolones for complicated urinary tract infections or when the upper urinary tract is involved. Antibiotics are rarely needed for the treatment of sinusitis. When indicated, a 5-day course should suffice. There is no consensus for the duration of antibiotic treatment in skin infections. The benefit of inflammation biomarkers to diminish the duration of antibiotics has not yet been established for common infections.

[Clostridium difficile: a serious outpatient infection?]. / Clostridium difficile: vers des infections graves en médecine ambulatoire?

Secondary to severe hospital outbreaks due to hypervirulent strains of Clostridium difficile, several surveillance systems in North-America and Europe observed an increase in infections due to this micro-organism, also in the outpatient setting. The case reported in the present article illustrates the fulminant presentation that a C. difficile colitis can show in a previously healthy person without prior contact with healthcare facilities. It introduces a review of some recent publications on the current changes in the epidemiology, clinical presentation, diagnosis and treatment of this disease.

Antibiotic use: is appropriateness expensive?

Antibiotics are prone to misuse. In this study, 37% of 600 antibiotic prescriptions in three hospitals were considered unnecessary. When antibiotic therapy was indicated, 45% were considered to be inadequate. In multivariate analyses, the indicated treatments were found to be more expensive than the unjustified ones, probably because the latter were more often oral regimens. However, for indicated treatments, the cost of adequate and inadequate treatments did not differ significantly.

Impact of participation in a surgical site infection surveillance network: results from a large international cohort study.

BACKGROUND: Surveillance of surgical site infections (SSIs) is a core component of effective infection control practices, though its impact has not been quantified on a large scale. AIM: To determine the time-trend of SSI rates in surveillance networks. METHODS: SSI surveillance networks provided procedure-specific data on numbers of SSIs and operations, stratified by hospitals' year of participation in the surveillance, to capture length of participation as an exposure. Pooled and procedure-specific random-effects Poisson regression was performed to obtain yearly rate ratios (RRs) with 95% confidence intervals (CIs), and including surveillance network as random intercept. FINDINGS: Of 36 invited networks, 17 networks from 15 high-income countries across Asia, Australia and Europe participated in the study. Aggregated data on 17 surgical procedures (cardiovascular, digestive, gynaecological-obstetrical, neurosurgical, and orthopaedic) were collected, resulting in data concerning 5,831,737 operations and 113,166 SSIs. There was a significant decrease in overall SSI rates over surveillance time, resulting in a 35% reduction at the ninth (final) included year of surveillance (RR: 0.65; 95% CI: 0.63-0.67). There were large variations across procedure-specific trends, but strong consistent decreases were observed for colorectal surgery, herniorrhaphy, caesarean section, hip prosthesis, and knee prosthesis. CONCLUSION: In this large, international cohort study, pooled SSI rates were associated with a stable and sustainable decrease after joining an SSI surveillance network; a causal relationship is possible, although unproven. There was heterogeneity in procedure-specific trends. These findings support the pivotal role of surveillance in reducing infection rates and call for widespread implementation of hospital-based SSI surveillance in high-income countries.

[New Swiss guidelines for the prevention of infective endocarditis]. / Nouvelles recommandations suisses pour ola prophylaxie de l'endocardite infectieuse.

Following the publication of updated American guidelines in 2007, the 2000 Swiss guidelines for the prevention of endocarditis have been revised. These new guidelines are more restrictive than the former ones. They include fewer cardiac conditions and fewer invasive procedures. Only patients at high risk of adverse outcome in case of endocarditis should now receive antibiotics before some invasive procedures.

[Urinary tract infection: a tailored diagnosis]. / Infection urinaire: un diagnostic sur mesure.

Urine dipstick testing reveals the presence of esterase secreted by leukocytes, and nitrites produced by some bacteria. The presence of either one confirms the diagnosis of acute uncomplicated urinary tract infection, that is in a woman of childbearing age with typical symptoms. Indeed, false positive tests are rare in this population. In contrast, dipstick testing is much less reliable in aged patients, and those with incontinence or an urinary catheter. Because asymptomatic bacteriuria is frequent in this population which, on the other hand, suffers more often from urinary tract infections due to bacteria that don't produce nitrites, the specificity and sensitivity of dipstick testing are low and should motivate a comprehensive approach to avoid unnecessary treatments or missed diagnoses.

Temporal trends and epidemiology of Staphylococcus aureus surgical site infection in the Swiss surveillance network: a cohort study.

BACKGROUND: Staphylococcus aureus is the leading pathogen in surgical site infections (SSI). AIM: To explore trends and risk factors associated with S. aureus SSI. METHODS: Risk factors for monomicrobial S. aureus SSI were identified from the Swiss multi-centre SSI surveillance system using multi-variate logistic regression. Both in-hospital and postdischarge SSI were identified using standardized definitions. FINDINGS: Over a six-year period, data were collected on 229,765 surgical patients, of whom 499 (0.22%) developed monomicrobial S. aureus SSI; 459 (92.0%) and 40 (8.0%) were due to meticillin-susceptible S. aureus (MSSA) and meticillin-resistant S. aureus (MRSA), respectively. There was a significant decrease in the rate of MSSA SSI (P = 0.007), but not in the rate of MRSA SSI (P = 0.70). Independent protective factors for S. aureus SSI were older age [≥75 years vs <50 years: odds ratio (OR) 0.60, 95% confidence interval (CI) 0.44-0.83], laparoscopy/minimally invasive surgery (OR 0.68, 95% CI 0.50-0.92), non-clean surgery [OR 0.78 (per increase in wound contamination class), 95% CI 0.64-0.94] and correct timing of pre-operative antibiotic prophylaxis (OR 0.80, 95% CI 0.65-0.98). Independent risk factors were male sex (OR 1.38, 95% CI 1.14-1.66), higher American Society of Anesthesiologists' score (per one-point increment: OR 1.30, 95% CI 1.13-1.51), re-operation for non-infectious reasons (OR 4.59, 95% CI 3.59-5.87) and procedure type: cardiac surgery, laminectomy, and hip or knee arthroplasty had two-to nine-fold increased odds of S. aureus SSI compared with other procedures. CONCLUSIONS: SSI due to S. aureus are decreasing and becoming rare events in Switzerland. High-risk procedures that may benefit from specific preventive measures were identified. Unfortunately, many of the independent risk factors are not easily modifiable.

[Tick-borne encephalitis, rabies, and echinococcosis in Switzerland]. / Encéphatite à tiques, rage et échinococcose: situation en Suisse.

Swiss guidelines have been published recently for Lyme disease, but three other zoonoses have motivated a particular attention lately because they cause or might cause illnesses in Switzerland. The incidence of tick-borne encephalitis is clearly increasing since 2004. The vaccination of persons living or residing temporally in risk areas is now routinely recommended. Although eradicated in wild mammals since 1996, rabies still constitutes a threat through bats and illegally imported pets. The epidemiology of echinococcosis is influenced by the increase in fox populations in urban areas. This could result in a higher prevalence of the disease in dogs and thus a higher risk of exposure for humans.

[Diagnosis and treatment of urethritis]. / Diagnostic et prise en charge de l'urétrite.

Clinical urethritis should motivate urine analyses including tests for leukocytes and PCR for C. trachomatis and N. gononhocae. The culture of an urethral swab for gonococci is sensitive as well. It allows susceptibility tests. Other infectious agents have been associated with urethritis (e.g., M. genitalium, T. vaginalis, H. simplex). They should be searched in case of negative first results or non-response to an empiric treatment. Given the emergence of resistances to quinolones, single doses of azithromycin 1 g plus cefixime 400 mg constitute a good choice which permits to ensure adherence. Contact tracing, screening for other sexually transmitted infections, and the evaluation of the sexual behaviour should always be done in order to prevent any further transmission.