Prospective case-control analysis of the aetiologies of acute undifferentiated fever in Vietnam

Acute undifferentiated fever (AUF) is frequently observed in tropical settings, but diagnosing the cause of AUF is often a challenge for local physicians and the physicians treating returning travellers. We conducted a case-control study in central Vietnam in 2016. A total of 378 febrile adult patients (AUFs) with a fever for ≤21 days, no evidence of localized infection and negative screening tests for dengue and malaria, and 384 afebrile adult patients (Controls) were prospectively enrolled. Whole blood, plasma, eschar swab, throat swab and urine specimens were collected and analysed. Quantitative PCR and RT-PCR were used to test for 55 bacteria, viruses and their subtypes. Serological tests were also used to test for rickettsial agents. The most common aetiology was influenza virus (20.9% in AUFs vs. 0% in Controls), followed by rickettsial agents (mainly Orientia tsutsugamushi and Rickettsia typhi) (10.8% vs. 0.3%), dengue virus (7.7% vs. 0.5%), Leptospira (4.8% vs. 0.8%), adenovirus (4.8% vs. 1.0%), and enterovirus (2.1% vs. 0%) (p < .05). The real proportion of dengue in AUF cases was underestimated because patients with dengue-positive rapid diagnosis tests were excluded from the study. The emerging agent Rickettsia felis, which had not been previously observed in Vietnam, was detected in this study. In total, 216 patients (57.1%) were given causative diagnoses, comprising 143 (66.2%) monoinfections and 73 (33.8%) coinfections. The infections caused by these agents should be considered in clinical practice and further studies. Additionally, agents susceptible to doxycycline were detected in 15.6% of AUFs; thus, this drug should be included in the panel used to treat AUF patients.

Investigations by the Institut Hospitalo-Universitaire Méditerranée Infection of food and food-borne infections in the Mediterranean Basin and in sub-Saharan Africa

Food-borne infections are major causes of public health concern in developing and developed countries. During the past decade, the Institut Hospitalo-Universitaire Méditerranée Infection has conducted or been involved in multiple investigations that aimed at identifying the sources and strains responsible for food-borne diseases and therefore at improving the understanding, diagnosis, prevention and control of these infections. Investigations were conducted in the Mediterranean area and in sub-Saharan Africa on more than 15 food-borne agents, 17 food products and 14 antibiotic resistance-associated genes. Multiple sources, including unexpected ones, and pathogens, including emerging ones, were involved. Travelling in developing countries and zoonoses are major contributors to food-borne infections, while food-borne transmission of resistance-associated genes is increasingly reported. However, risk factors and pathogens associated with food-borne infections likely remain untapped and must be more extensively investigated, monitored and regularly reassessed. Diagnostic tests based on new technologies and real-time surveillance tools based on microbiology laboratory data are promising approaches to detect known food-borne infections and decipher new ones. Studies of the microbiota and its relationships with dietary patterns are also worth being conducted.

Extremely and pandrug-resistant bacteria extra-deaths: myth or reality?

In 2009, the European Centre for Disease Prevention and Control (ECDC) estimated that multidrug-resistant (MDR) bacterial infections were responsible for 25,000 extra-deaths per year. In 2015, another report estimated that 12,500 extra-deaths were attributable to MDR bacteria every year in France. Recently, the United Nations claimed that resistance to antimicrobials was a global scourge, forecasting 10 million deaths in 2050. Surprisingly, our antibiotic resistance surveillance system in Marseille, France, did not allowed us to observe similar trends. We herein compared our data on extremely drug-resistant (XDR)/pandrug-resistant (PDR) patient extra-deaths to evaluations and predictions from these reports. First, we retrospectively collect and analyze antibiotic resistance data produced by our settings between November 2009 and March 2015 to look for 30-day deaths attributable to XDR/PDR strains belonging to 11 bacterial species/genus. In parallel, we performed a PubMed literature search to look for articles published prior to July 2016 and describing human deaths due to PDR strains. Overall, 35,723 patients were infected by at least one bacterial species/genus of interest and 85 by XDR/PDR strains. Of these patients, only one death was attributable to a XDR bacterial infection in a patient with strong comorbidities and two consecutive septic shocks. Our literature review shows that only four articles described human deaths due to PDR bacteria. All together, these data allowed us to conclude that there is a large discrepancy between the real count of deaths attributable to XDR/PDR bacteria and alarmist predictions.

Parallel Decline of Malaria and Rickettsia felis Infections in Senegal

Rickettsia felis is a common emerging pathogen in sub-Saharan Africa. Comparing dynamics of morbidities due to malaria and R. felis infections in two Senegalese villages, we found a strong and significant correlation between them. Malaria morbidity is strongly decreasing because of the implementation of long-lasting insecticidal nets, so we hypothesize that the same measure may decrease the R. felis infections.

Evaluating the Clinical Burden and Mortality Attributable to Antibiotic Resistance: The Disparity of Empirical Data and Simple Model Estimations

Given the proliferation of cataclysmic predictions about antibiotic resistance, cases of which are estimated to amount to 12500 per year in France, we herein decided to compare the empirical clinical microbiology data from our institution with estimates and predictions from 10 major international scientific articles and reports. The analysis of 7 years of antibiotic resistance data from 10 bacterial species and genera of clinical interest from our institution identified no deaths that were directly attributable to extremely drug-resistant bacteria. By comparing our observations to the 10 articles and reports studied herein, we concluded that their results lack empirical data. Interventions are urgently needed to significantly reduce both mortality and the healthcare costs associated with bacterial infections, including the implementation of local and national laboratory data-based surveillance systems for the routine surveillance of antibiotic resistance that would be helpful for a better understanding of how to manage antibiotic-resistant bacteria in the future.

Implementation and Initial Analysis of a Laboratory-Based Weekly Biosurveillance System, Provence-Alpes-Côte d'Azur, France

We describe the implementation of an automated infectious disease surveillance system that uses data collected from 210 microbiologic laboratories throughout the Provence-Alpes-Côte d’Azur region in France. Each week, these facilities report bacterial species that have been isolated from patients in their area. An alarm is triggered whenever the case count for a bacterial species infection exceeds 2 SDs of the historical mean for that species at the participating laboratory. At its inception in July 2013, the system monitored 611 bacterial species. During July 1, 2013–March 20, 2016, weekly analyses of incoming surveillance data generated 34 alarms signaling possible infectious disease outbreaks; after investigation, 14 (41%) of these alarms resulted in health alerts declared by the regional health authority. We are currently improving the system by developing an Internet-based surveillance platform and extending our surveillance to include more laboratories in the region.

Implementation of Syndromic Surveillance Systems in Two Rural Villages in Senegal

Infectious diseases still represent a major challenge for humanity. In this context, their surveillance is critical. From 2010 to 2016, two Point-Of-Care (POC) laboratories have been successfully implemented in the rural Saloum region of Senegal. In parallel, a homemade syndromic surveillance system called EPIMIC was implemented to monitor infectious diseases using data produced by the POC laboratory of the Timone hospital in Marseille, France. The aim of this study is to describe the steps necessary for implementing EPIMIC using data routinely produced by two POC laboratories (POC-L) established in rural Senegal villages. After improving EPIMIC, we started to monitor the 15 pathogens routinely diagnosed in the two POC-L using the same methodology we used in France. In 5 years, 2,577 deduplicated patients-samples couples from 775 different patients have been tested in the Dielmo and Ndiop POC-L. 739 deduplicated patients-samples couples were found to be positive to at least one of the tested pathogens. The retrospective analysis of the Dielmo and Ndiop POC data with EPIMIC allowed to generate 443 alarms. Since January 2016, 316 deduplicated patients-samples couples collected from 298 different patients were processed in the Niakhar POC laboratory. 56 deduplicated patients-samples couples were found to be positive to at least one of the tested pathogens. The retrospective analysis of the data of the Niakhar POC laboratory with EPIMIC allowed to generate 14 alarms. Although some improvements are still needed, EPIMIC has been successfully spread using data routinely produced by two rural POC-L in Senegal, West Africa.

Enterococcus faecalis urinary-tract infections: Do they have a zoonotic origin?

Major human pathogens are frequently isolated from meat-producing animals, particularly poultry. Among them is Enterococcus faecalis, which is known to be one of the main cause of human urinary-tract infections worldwide. Early in 2015, we detected several, consecutive abnormal increases in the weekly number of human E. faecalis infections in various medical settings in the Provence-Alpes-Côte d'Azur region of France, especially including community-acquired urinary-tract infections. Speculating that this region-wide epidemiological event may have originated from animal-based food, we initiated this work to provide an overview of the epidemiology of E. faecalis, with a particular focus on the possible link between E. faecalis clones isolated from food-producing animals and those responsible for human urinary-tract infections. At that time, only one study had clearly identified strong epidemiological links between E. faecalis clones isolated from food-producing animals and human E. faecalis urinary-tract infections. This observation, coupled with our region-wide epidemiological experience, leads us to strongly believe that E. faecalis is a real zoonotic pathogen with potentially highly significant impact on human health. This is of particular concern because of its ability to acquire antibiotic-resistance genes and to infect animals and humans. Various strategies must be urgently implemented to address this public health threat, in particular through the development and implementation of large integrated automated surveillance systems based on animal and human health data to enable us to detect E. faecalis epidemiological events.

Traditional and syndromic surveillance of infectious diseases and pathogens

BACKGROUND

Infectious diseases remain a major public health problem worldwide. Hence, their surveillance is critical. Currently, many surveillance strategies and systems are in use around the world. An inventory of the data, surveillance strategies, and surveillance systems developed worldwide for the surveillance of infectious diseases is presented herein, with emphasis on the role of the microbiology laboratory in surveillance.

METHODS

The data, strategies, and systems used around the world for the surveillance of infectious diseases and pathogens, along with current issues and trends, were reviewed.

RESULTS

Twelve major classes of data were identified on the basis of their timing relative to infection, resources available, and type of surveillance. Two primary strategies were compared: disease-specific surveillance and syndromic surveillance. Finally, 262 systems implemented worldwide for the surveillance of infections were registered and briefly described, with a focus on those based on microbiological data from laboratories.

CONCLUSIONS

There is currently a wealth of available data on infections, which has been growing with the recent emergence of new technologies. Concurrently with the expansion of computer resources and networks, these data will allow the optimization of real-time detection and notification of infections.

Decreasing level of resistance in invasive Klebsiella pneumoniae strains isolated in Marseille, January 2012-July 2015

Background

Klebsiella pneumoniae is a Gram-negative bacterial species well known for its capacity to cause infections in humans, and to carry and spread a wide variety of resistance genes including extended-spectrum beta-lactamase genes, carbapenem resistance genes, and colistin resistance genes. Recently, our real-time laboratory-based surveillance system MARSS (the Marseille Antibiotic Resistance Surveillance System) allowed us to observe a intringing dramatic decrease in the beta-lactam resistance level of the K. pneumoniae strains routinely isolated from patients hospitalized in our settings since 2013. Here we study the evolution of the prevalence of K. pneumoniae infections in Marseille university hospitals, France, from January 2012 to July 2015, and study their antibiotic resistance profiles.

Methods

We collected data referring to patients hostpitalized for K. pneumoniae infections in the 4 university hospitals of Marseille from January 2012 to July 2015. We then study their antibiotic resistance profiles according the clinical sites from which each strain was collected. Antibiotic consumption data from our four hospitals were also analyzed from January 2013 to July 2015.

Results

Overall, 4868 patients were admitted in our settings for K. pneumoniae infections over the study period. Overall, 40.1, 22.3, 25.6, 0.4, 29.9, 14.8, 27.3 and 37.0 % of the strains were resistant to amoxicillin plus clavulanic acid, piperacillin-tazobactam, ceftriaxone, imipenem, ciprofloxacin, gentamicin, trimethoprim-sulfamethoxazole and furan, respectively. 447 were invasive infections. The resistance level of our invasive strains was significantly lower than that presented by 11, 7, 10 and 11 other European countries included in the 2013 European Antimicrobial Resistance Surveillance Network report for ceftriaxone, imipenem, ciprofloxacin and gentamicin, respectively, but significantly higher than that of 13, 1, 17 and 13 European countries for the same antibiotics. We also observed that the percentages of resistance of our invasive strains to three of the four antibiotics decreased over the study. In parallel, antibiotic consumption remained stable in our four hospitals from January 2013 to July 2015.

Conclusions

Altogether, our results underline that automated antibiotic-susceptibility testing results-based surveillance systems are crucial to better understand the evolving epidemiology of dangerous pathogenic bacterial species, like K. pneumoniae, at local scales.

Electronic supplementary material

The online version of this article (doi:10.1186/s40064-016-2296-0) contains supplementary material, which is available to authorized users.

Citrobacter amalonaticus human urinary tract infections, Marseille, France

Citrobacter amalonaticus is a bacterium that has rarely been reported as a human pathogen. Here we report four cases of C. amalonaticus infections occurring in patients hospitalized in Marseille, France, and review all cases described in the published literature.

EPIMIC: A Simple Homemade Computer Program for Real-Time EPIdemiological Surveillance and Alert Based on MICrobiological Data

BACKGROUND AND AIMS

Infectious diseases (IDs) are major causes of morbidity and mortality and their surveillance is critical. In 2002, we implemented a simple and versatile homemade tool, named EPIMIC, for the real-time systematic automated surveillance of IDs at Marseille university hospitals, based on the data from our clinical microbiology laboratory, including clinical samples, tests and diagnoses.

METHODS

This tool was specifically designed to detect abnormal events as IDs are rarely predicted and modeled. EPIMIC operates using Microsoft Excel software and requires no particular computer skills or resources. An abnormal event corresponds to an increase above, or a decrease below threshold values calculated based on the mean of historical data plus or minus 2 standard deviations, respectively.

RESULTS

Between November 2002 and October 2013 (11 years), 293 items were surveyed weekly, including 38 clinical samples, 86 pathogens, 79 diagnosis tests, and 39 antibacterial resistance patterns. The mean duration of surveillance was 7.6 years (range, 1 month-10.9 years). A total of 108,427 Microsoft Excel file cells were filled with counts of clinical samples, and 110,017 cells were filled with counts of diagnoses. A total of 1,390,689 samples were analyzed. Among them, 172,180 were found to be positive for a pathogen. EPIMIC generated a mean number of 0.5 alert/week on abnormal events.

CONCLUSIONS

EPIMIC proved to be efficient for real-time automated laboratory-based surveillance and alerting at our university hospital clinical microbiology laboratory-scale. It is freely downloadable from the following URL: http://www.mediterranee-infection.com/article.php?larub=157&titre=bulletin-epidemiologique (last accessed: 20/11/2015).

Facklamia hominis scapula abscess, Marseille, France

Facklamia hominis is a Gram-positive bacterium that was first isolated from various human samples, excluding abscesses of the scapula. We here report the first scapular abscess infection due to F. hominis, found in Marseille, France. We also reviewed all cases published in the literature.

Molecular epidemiology and distribution of serotypes, genotypes, and antibiotic resistance genes of Streptococcus agalactiae clinical isolates from Guelma, Algeria and Marseille, France

This study describes, for the first time, the genetic and phenotypic diversity among 93 Streptococcus agalactiae (group B Streptococcus, GBS) isolates collected from Guelma, Algeria and Marseille, France. All strains were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The molecular support of antibiotic resistance and serotyping were investigated by polymerase chain reaction (PCR). The phylogenetic lineage of each GBS isolate was determined by multilocus sequence typing (MLST) and grouped into clonal complexes (CCs) using eBURST. The isolates represented 37 sequence types (STs), 16 of which were novel, grouped into five CCs, and belonging to seven serotypes. Serotype V was the most prevalent serotype in our collection (44.1%). GBS isolates of each serotype were distributed among multiple CCs, including cps III/CC19, cps V/CC1, cps Ia/CC23, cps II/CC10, and cps III/CC17. All isolates presented susceptibility to penicillin, whereas resistance to erythromycin was detected in 40% and tetracycline in 82.2% of isolates. Of the 37 erythromycin-resistant isolates, 75.7% showed the macrolide-lincosamide-streptogramin B (MLSB)-resistant phenotype and 24.3% exhibited the macrolide (M)-resistant phenotype. Constitutive MLSB resistance (46%) mediated by the ermB gene was significantly associated with the Guelma isolates, whereas the M resistance phenotype (24.3%) mediated by the mefA/E gene dominated among the Marseille isolates and belonged to ST-23. Tetracycline resistance was predominantly due to tetM, which was detected alone (95.1%) or associated with tetO (3.7%). These results provide epidemiological data in these regions that establish a basis for monitoring increased resistance to erythromycin and also provide insight into correlations among clones, serotypes, and resistance genes.

Low Level of Resistance in Enterococci Isolated in Four Hospitals, Marseille, France

Enterococci are gram-positive cocci responsible for various infections worldwide, and their prevalence of antibiotic resistance greatly varies worldwide. This study investigates the prevalence of resistance to antibiotics in enterococci from patients admitted in the four university hospitals of Marseille between January 2013 and September 2014. Two thousand nine hundred seventy-six patients-bacteria couples were identified (2,507 Enterococcus faecalis and 469 Enterococcus faecium) in the four university hospitals of Marseille. 1.3%, 8.9%, 1.4%, and 0% of E. faecalis strains were resistant to amoxicillin, gentamicin, teicoplanin, and vancomycin, respectively, and 83.9%, 49.2%, 1.3%, and 0.2% of E. faecium strains were resistant to amoxicillin, gentamicin, teicoplanin, and vancomycin, respectively. Resistance to aminoglycosides and vancomycin in strains isolated from blood cultures was significantly lower than that of most European countries included in the 2012 European Antimicrobial Resistance Surveillance Network report. Our low percentage of antibiotic resistance in enterococci is likely due to a low level of E. faecium infections, underlining the need to implement surveillance systems, especially to monitor the E. faecalis/E. faecium ratio evolution in blood cultures and others.

Real-Time Microbiology Laboratory Surveillance System to Detect Abnormal Events and Emerging Infections, Marseille, France

Infectious diseases are a major threat to humanity, and accurate surveillance is essential. We describe how to implement a laboratory data-based surveillance system in a clinical microbiology laboratory. Two historical Microsoft Excel databases were implemented. The data were then sorted and used to execute the following 2 surveillance systems in Excel: the Bacterial real-time Laboratory-based Surveillance System (BALYSES) for monitoring the number of patients infected with bacterial species isolated at least once in our laboratory during the study periodl and the Marseille Antibiotic Resistance Surveillance System (MARSS), which surveys the primary β-lactam resistance phenotypes for 15 selected bacterial species. The first historical database contained 174,853 identifications of bacteria, and the second contained 12,062 results of antibiotic susceptibility testing. From May 21, 2013, through June 4, 2014, BALYSES and MARSS enabled the detection of 52 abnormal events for 24 bacterial species, leading to 19 official reports. This system is currently being refined and improved.

Enterococcus cecorum human infection, France

Enterococcus cecorum is a bacterium of the intestinal tract of many domestic animals that is rarely reported as human pathogen. Here we report the first case of incisional hernia plate infection and the first case of urinary tract colonization due to E. cecorum from patients in Marseille, France.

Ketamine effects on bupivacaine local anaesthetic activity and pharmacokinetics of bupivacaine in mice

This study was designed to document possible changes in bupivacaine (B) local anaesthetic activity and pharmacokinetics in mice after a ketamine (K) injection. In the experiments, bupivacaine (8.25 mg.kg(-1)), was injected into the popliteal space of the right posterior limb: the local anaesthetic activity was assessed according to a sciatic nerve blockade method with three different doses (2, 10 and 40 mg/kg) of ketamine and the kinetics were studied after a 10 mg/kg dose. When ketamine was associated, the local anesthetic activity of bupivacaine was significantly enhanced as well as its elimination half-life. Significantly lower levels of the main metabolite, PPX, were observed, when ketamine was associated, suggesting a metabolic inhibition phenomenon. The ketamine-induced increase in the total anaesthetic effect of bupivacaine may thus be explained by kinetic modifications i.e. a possible inhibiting effect of ketamine on the metabolism of bupivacaine.