Outbreak of Listeriosis in South Africa Associated with Processed Meat.

BACKGROUND: An outbreak of listeriosis was identified in South Africa in 2017. The source was unknown. METHODS: We conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type Listeria monocytogenes isolates. A case was defined as laboratory-confirmed L. monocytogenes infection during the period from June 11, 2017, to April 7, 2018. RESULTS: A total of 937 cases were identified, of which 465 (50%) were associated with pregnancy; 406 of the pregnancy-associated cases (87%) occurred in neonates. Of the 937 cases, 229 (24%) occurred in patients 15 to 49 years of age (excluding those who were pregnant). Among the patients in whom human immunodeficiency virus (HIV) status was known, 38% of those with pregnancy-associated cases (77 of 204) and 46% of the remaining patients (97 of 211) were infected with HIV. Among 728 patients with a known outcome, 193 (27%) died. Clinical isolates from 609 patients were sequenced, and 567 (93%) were identified as sequence type 6 (ST6). In a case-control analysis, patients with ST6 infections were more likely to have eaten polony (a ready-to-eat processed meat) than those with non-ST6 infections (odds ratio, 8.55; 95% confidence interval, 1.66 to 43.35). Polony and environmental samples also yielded ST6 isolates, which, together with the isolates from the patients, belonged to the same core-genome multilocus sequence typing cluster with no more than 4 allelic differences; these findings showed that polony produced at a single facility was the outbreak source. A recall of ready-to-eat processed meat products from this facility was associated with a rapid decline in the incidence of L. monocytogenes ST6 infections. CONCLUSIONS: This investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons. Whole-genome sequencing facilitated the detection of the outbreak and guided the trace-back investigations that led to the identification of the source.

Foodborne botulism outbreak involving different nationalities during the Rugby World Cup: critical role of credit card data and rapid international cooperation, France, September 2023.

In September 2023, a severe outbreak of type B botulism with fifteen cases was linked to consumption of canned sardines at a restaurant in Bordeaux, France, during the Rugby World Cup. The cases were from seven countries. One death was recorded. Outbreak investigation using credit card data, rapid communication between health authorities of the affected countries and broad media communication allowed identification of cases and exposed persons and prevented further severe outcomes.

National perinatal survey demonstrates a decreasing seroprevalence of Toxoplasma gondii infection among pregnant women in France, 1995 to 2016: impact for screening policy.

BackgroundToxoplasmosis during pregnancy can result in congenital anomalies or fetal death. Universal antenatal screening is recommended in France, a strategy in place since the 1970s.AimWe determined the seroprevalence of toxoplasmosis among pregnant women participating in the 2016 national perinatal survey (ENP), compared results with previous ENPs, and investigated factors associated with Toxoplasma gondii infection.MethodsUsing the 2016 ENP data, which contain sociodemographic and clinical information from all women giving birth during a one week period, we calculated adjusted prevalence ratios (aPR) by sociodemographic factors. Using available data from prior ENPs (1995, 2003 and 2010), we calculated age-standardised seroprevalences and aPRs for French women.ResultsIn 2016, seroprevalence was 31.3% overall. Among French women, associations with increasing age (aPR: 1.54; 95% CI: 1.39-1.70), residence in Paris (aPR: 1.19; 95% CI: 1.08-1.31) or south-western regions (aPR: 1.19; 95% CI: 1.08-1.31), and higher professional status (aPR: 1.12; 95%CI 1.04-1.21) were observed. An association with increasing age was also evident among women from North Africa and sub-Saharan Africa. Age-standardised seroprevalence decreased from 55.0% in 1995 to 33.7% in 2016. Among French women, significant associations with age, Paris and south-west regions persisted across all ENPs.ConclusionHigher prevalences in older women may reflect a higher past risk of exposure while persistent geographical differences may reflect dietary or environmental differences. Toxoplasma seroprevalence among pregnant women continues to fall and will impact screening effectiveness. This warrants a comprehensive review to determine the appropriate future of prevention in France.

Accuracy of Emergency Department Clinical Findings for Diagnosis of Coronavirus Disease 2019.

STUDY OBJECTIVE: We seek to describe the medical history and clinical findings of patients attending the emergency department (ED) with suspected coronavirus disease 2019 (COVID-19) and estimate the diagnostic accuracy of patients' characteristics for predicting COVID-19. METHODS: We prospectively enrolled all patients tested for severe acute respiratory syndrome coronavirus 2 by reverse-transcriptase polymerase chain reaction in our ED from March 9, 2020, to April 4, 2020. We abstracted medical history, physical examination findings, and the clinical probability of COVID-19 (low, moderate, and high) rated by emergency physicians, depending on their clinical judgment. We assessed diagnostic accuracy of these characteristics for COVID-19 by calculating positive and negative likelihood ratios. RESULTS: We included 391 patients, of whom 225 had positive test results for severe acute respiratory syndrome coronavirus 2. Reverse-transcriptase polymerase chain reaction result was more likely to be negative when the emergency physician thought that clinical probability was low, and more likely to be positive when he or she thought that it was high. Patient-reported anosmia and the presence of bilateral B lines on lung ultrasonography had the highest positive likelihood ratio for the diagnosis of COVID-19 (7.58, 95% confidence interval [CI] 2.36 to 24.36; and 7.09, 95% CI 2.77 to 18.12, respectively). The absence of a high clinical probability determined by the emergency physician and the absence of bilateral B lines on lung ultrasonography had the lowest negative likelihood ratio for the diagnosis of COVID-19 (0.33, 95% CI 0.25 to 0.43; and 0.26, 95% CI 0.15 to 0.45, respectively). CONCLUSION: Anosmia, emergency physician estimate of high clinical probability, and bilateral B lines on lung ultrasonography increased the likelihood of identifying COVID-19 in patients presenting to the ED.

Ongoing nationwide outbreak of Salmonella Agona associated with internationally distributed infant milk products, France, December 2017.

On 1 December 2017, an outbreak of Salmonella Agona infections among infants was identified in France. To date, 37 cases (median age: 4 months) and two further international cases have been confirmed. Five different infant milk products manufactured at one facility were implicated. On 2 and 10 December, the company recalled the implicated products; on 22 December, all products processed at the facility since February 2017. Trace-forward investigations indicated product distribution to 66 countries.

Estimated Annual Numbers of Foodborne Pathogen-Associated Illnesses, Hospitalizations, and Deaths, France, 2008-2013.

Estimates of the annual numbers of foodborne illnesses and associated hospitalizations and deaths are needed to set priorities for surveillance, prevention, and control strategies. The objective of this study was to determine such estimates for 2008-2013 in France. We considered 15 major foodborne pathogens (10 bacteria, 3 viruses, and 2 parasites) and estimated that each year, the pathogens accounted for 1.28-2.23 million illnesses, 16,500-20,800 hospitalizations, and 250 deaths. Campylobacter spp., nontyphoidal Salmonella spp., and norovirus accounted for >70% of all foodborne pathogen-associated illnesses and hospitalizations; nontyphoidal Salmonella spp. and Listeria monocytogenes were the main causes of foodborne pathogen-associated deaths; and hepatitis E virus appeared to be a previously unrecognized foodborne pathogen causing ≈68,000 illnesses in France every year. The substantial annual numbers of foodborne illnesses and associated hospitalizations and deaths in France highlight the need for food-safety policymakers to prioritize foodborne disease prevention and control strategies.

Real-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes, France.

During 2015-2016, we evaluated the performance of whole-genome sequencing (WGS) as a routine typing tool. Its added value for microbiological and epidemiologic surveillance of listeriosis was compared with that for pulsed-field gel electrophoresis (PFGE), the current standard method. A total of 2,743 Listeria monocytogenes isolates collected as part of routine surveillance were characterized in parallel by PFGE and core genome multilocus sequence typing (cgMLST) extracted from WGS. We investigated PFGE and cgMLST clusters containing human isolates. Discrimination of isolates was significantly higher by cgMLST than by PFGE (p<0.001). cgMLST discriminated unrelated isolates that shared identical PFGE profiles and phylogenetically closely related isolates with distinct PFGE profiles. This procedure also refined epidemiologic investigations to include only phylogenetically closely related isolates, improved source identification, and facilitated epidemiologic investigations, enabling identification of more outbreaks at earlier stages. WGS-based typing should replace PFGE as the primary typing method for L. monocytogenes.

Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017.

In August 2017, an outbreak of six listeriosis cases in Denmark was traced to cold-smoked salmon, using epidemiological investigations and whole-genome sequencing (WGS) analyses. Exchange of genome sequences allowed identification in France of a food isolate from a salmon-derived product and a human isolate from 2016 within the same cgMLST cluster as the Danish isolates (L2-SL8-ST8-CT771). The salmon product came from a third European Union country. WGS can rapidly link human cases and food isolates across Europe.

Escherichia coli O157:H7 infections associated with consumption of locally grown strawberries contaminated by deer.

BACKGROUND: An outbreak of Escherichia coli O157:H7 was identified in Oregon through an increase in Shiga toxin-producing E. coli cases with an indistinguishable, novel pulsed-field gel electrophoresis (PFGE) subtyping pattern. METHODS: We defined confirmed cases as persons from whom E. coli O157:H7 with the outbreak PFGE pattern was cultured during July-August 2011, and presumptive cases as persons having a household relationship with a case testing positive for E. coli O157:H7 and coincident diarrheal illness. We conducted an investigation that included structured hypothesis-generating interviews, a matched case-control study, and environmental and traceback investigations. RESULTS: We identified 15 cases. Six cases were hospitalized, including 4 with hemolytic uremic syndrome (HUS). Two cases with HUS died. Illness was significantly associated with strawberry consumption from roadside stands or farmers' markets (matched odds ratio, 19.6; 95% confidence interval, 2.9-∞). A single farm was identified as the source of contaminated strawberries. Ten of 111 (9%) initial environmental samples from farm A were positive for E. coli O157:H7. All samples testing positive for E. coli O157:H7 contained deer feces, and 5 tested farm fields had ≥ 1 sample positive with the outbreak PFGE pattern. CONCLUSIONS: The investigation identified fresh strawberries as a novel vehicle for E. coli O157:H7 infection, implicated deer feces as the source of contamination, and highlights problems concerning produce contamination by wildlife and regulatory exemptions for locally grown produce. A comprehensive hypothesis-generating questionnaire enabled rapid identification of the implicated product. Good agricultural practices are key barriers to wildlife fecal contamination of produce.

Fatal neonatal listeriosis following L. monocytogenes horizontal transmission highlights neonatal susceptibility to orally acquired listeriosis.

We report a case of fulminant fatal neonatal listeriosis due to horizontal transmission of Listeria monocytogenes (Lm) in a neonatal double room. Genomic analyses reveal a close genetic relationship between clinical isolates, supporting cross-contamination. Oral inoculation experiments in adult and neonatal mice show that neonates are susceptible to a low Lm inoculum and that this susceptibility results from the immaturity of the neonatal gut microbiota. Infected neonates should therefore be isolated for as long as they shed Lm in their feces to avoid horizontal transmission and its dire consequences.

Multinational Outbreak of Listeria monocytogenes Infections Linked to Enoki Mushrooms Imported from the Republic of Korea 2016-2020.

Keeping the global food supply safe necessitates international collaborations between countries. Health and regulatory agencies routinely communicate during foodborne illness outbreaks, allowing partners to share investigational evidence. A 2016-2020 outbreak of Listeria monocytogenes infections linked to imported enoki mushrooms required a multinational collaborative investigation among the United States, Canada, Australia, and France. Ultimately, this outbreak included 48 ill people, 36 in the United States and 12 in Canada, and was linked to enoki mushrooms sourced from one manufacturer located in the Republic of Korea. Epidemiologic, laboratory, and traceback evidence led to multiple regulatory actions, including extensive voluntary recalls by three firms in the United States and one firm in Canada. In the United States and Canada, the Korean manufacturer was placed on import alert while other international partners provided information about their respective investigations and advised the public not to eat the recalled enoki mushrooms. The breadth of the geographic distribution of this outbreak emphasizes the global reach of the food industry. This investigation provides a powerful example of the impact of national and international coordination of efforts to respond to foodborne illness outbreaks and protect consumers. It also demonstrates the importance of fast international data sharing and collaboration in identifying and stopping foodborne outbreaks in the global community. Additionally, it is a meaningful example of the importance of food sampling, testing, and integration of sequencing results into surveillance databases.

Misidentification of Yersinia pestis by automated systems, resulting in delayed diagnoses of human plague infections--Oregon and New Mexico, 2010-2011.

One human plague case was reported in Oregon in September 2010 and another in New Mexico in May 2011. Misidentification of Yersinia pestis by automated identification systems contributed to delayed diagnoses for both cases.

A new SARS-CoV-2 variant with high lethality poorly detected by RT-PCR on nasopharyngeal samples: an observational study.

OBJECTIVES: In early January 2021 an outbreak of nosocomial cases of coronavirus disease 2019 (COVID-19) emerged in Western France; RT-PCR tests were repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole-genome sequencing (WGS) revealed a new variant, currently defining a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.616. In March, the WHO classified this as a 'variant under investigation' (VUI). We analysed the characteristics and outcomes of COVID-19 cases related to this new variant. METHODS: Clinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled those inpatients with: (a) positive SARS-CoV-2 RT-PCR on a respiratory sample, (b) seroconversion with anti-SARS-CoV-2 IgG/IgM, or (c) suggestive symptoms and typical features of COVID-19 on a chest CT scan. Cases were categorized as B.1.616, a variant of concern (VOC), or unknown. RESULTS: From 1st January to 24th March 2021, 114 patients fulfilled the inclusion criteria: B.1.616 (n = 39), VOC (n = 32), and unknown (n = 43). B.1.616-related cases were older than VOC-related cases (81 years, interquartile range (IQR) 73-88 versus 73 years, IQR 67-82, p < 0.05) and their first RT-PCR tests were rarely positive (6/39, 15% versus 31/32, 97%, p < 0.05). The B.1.616 variant was independently associated with severe disease (multivariable Cox model HR 4.0, 95%CI 1.5-10.9) and increased lethality (28-day mortality 18/39 (46%) for B.1.616 versus 5/32 (16%) for VOC, p = 0.006). CONCLUSION: We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, which is poorly detected by RT-PCR on nasopharyngeal samples and is associated with high lethality.

Enteric fever among children: 50 cases in a French tertiary care centre.

Background: Enteric fever in France is primarily travel-associated. Characteristics of paediatric cases are scarce and information from field studies in endemic countries might not be generalizable to non-endemic countries. Methods: In this retrospective study, we reviewed all cases of typhoid and paratyphoid fever treated in a French paediatric tertiary care centre from 1993 to 2015. Results: Fifty cases of enteric fever due to Salmonella enterica serovar Typhi (n = 44) and Paratyphi (n = 6) were identified. Sixty-one percent of the children had travelled to Africa and 34% to the Indian subcontinent. Among travel-associated cases, 85% were visiting friends and relatives (VFR). Ninety-six percent had high fever associated with gastrointestinal symptoms. Anaemia (66%), elevated C-reactive protein (80%), transaminitis (87%) and mild hyponatremia (50%) were the main biological findings. Blood cultures were positive in 90% of cases. Twelve strains (24%) were resistant at least to one antibiotic, and all of them had been isolated since 2003, increasing the resistance rate during this last period to 43% (12/28). Ceftriaxone was administered to 71 patients for a median duration of 6 days (interquartile range (IQR): 4-8). The median time to apyrexia after the onset of treatment was 4 days (IQR: 2-5 days). Complications occurred in nine children with five (10%) presenting neurologic disorders. All 50 patients recovered. Conclusion: In France, paediatric enteric fever is mainly a travel-associated disease and occurs in patients returning from a prolonged stay in an endemic area. Children VFR are at high risk and should be a priority target group for pre-travel preventive measures. The increase in antibiotic resistance reflects the situation in endemic countries and is a major concern.

Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species.

Horizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR). However, the dynamics of AMR transfer through bacterial populations and its direct impact on human disease is poorly elucidated. Here, we study parallel epidemic emergences of multiple Shigella species, a priority AMR organism, in men who have sex with men to gain insight into AMR emergence and spread. Using genomic epidemiology, we show that repeated horizontal transfer of a single AMR plasmid among Shigella enhanced existing and facilitated new epidemics. These epidemic patterns contrasted with slighter, slower increases in disease caused by organisms with vertically inherited (chromosomally encoded) AMR. This demonstrates that horizontal transfer of AMR directly affects epidemiological outcomes of globally important AMR pathogens and highlights the need for integration of genomic analyses into all areas of AMR research, surveillance and management.

Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance.

Shigella are globally important diarrhoeal pathogens that are endemic in low-to-middle income nations and also occur in high income nations, typically in travellers or community-based risk-groups. Shigella phylogenetics reveals population structures that are more reliable than those built with traditional typing methods, and has identified sublineages associated with specific geographical regions or patient groups. Genomic analyses reveal temporal increases in Shigella antimicrobial resistance (AMR) gene content, which is frequently encoded on mobile genetic elements. Here, we whole genome sequenced representative subsamples of S. flexneri 2a and S. sonnei (n = 366) from the United Kingdom from 2008 to 2014, and analysed these alongside publicly available data to make qualitative insights on the genomic epidemiology of shigellosis and its AMR within the broader global context. Combined phylogenetic, epidemiological and genomic anlayses revealed the presence of domestically-circulating sublineages in patient risk-groups and the importation of travel-related sublineages from both Africa and Asia, including ciprofloxacin-resistant sublineages of both species from Asia. Genomic analyses revealed common AMR determinants among travel-related and domestically-acquired isolates, and the evolution of mutations associated with reduced quinolone susceptibility in domestically-circulating sublineages. Collectively, this study provides unprecedented insights on the contribution and mobility of endemic and travel-imported sublineages and AMR determinants responsible for disease in a high-income nation.

Clinical features and prognostic factors of listeriosis: the MONALISA national prospective cohort study.

BACKGROUND: Listeriosis is a severe foodborne infection and a notifiable disease in France. We did a nationwide prospective study to characterise its clinical features and prognostic factors. METHODS: MONALISA was a national prospective observational cohort study. We enrolled eligible cases declared to the National Reference Center for Listeria (all microbiologically proven) between Nov 3, 2009, and July 31, 2013, in the context of mandatory reporting. The outcomes were analysis of clinical features, characterisation of Listeria isolates, and determination of predictors of 3-month mortality or persisting impairment using logistic regression. A hierarchical clustering on principal components was also done for neurological and bacteraemic cases. The study is registered at ClinicalTrials.gov, number NCT01520597. FINDINGS: We enrolled 818 cases from 372 centres, including 107 maternal-neonatal infections, 427 cases of bacteraemia, and 252 cases of neurolisteriosis. Only five (5%) of 107 pregnant women had an uneventful outcome. 26 (24%) of 107 mothers experienced fetal loss, but never after 29 weeks of gestation or beyond 2 days of admission to hospital. Neurolisteriosis presented as meningoencephalitis in 212 (84%) of 252 patients; brainstem involvement was only reported in 42 (17%) of 252 patients. 3-month mortality was higher for bacteraemia than neurolisteriosis (hazard ratio [HR] 0·54 [95% CI 0·41-0·69], p<0·0001). For both bacteraemia and neurolisteriosis, the strongest mortality predictors were ongoing cancer (odds ratio [OR] 5·19 [95% CI 3·01-8·95], p<0·0001), multi-organ failure (OR 7·98 [4·32-14·72], p<0·0001), aggravation of any pre-existing organ dysfunction (OR 4·35 [2·79-6·81], p<0·0001), and monocytopenia (OR 3·70 [1·82-7·49], p=0·0003). Neurolisteriosis mortality was higher in blood-culture positive patients (OR 3·67 [1·60-8·40], p=0·002) or those receiving adjunctive dexamethasone (OR 4·58 [1·50-13·98], p=0·008). INTERPRETATION: The severity of listeriosis is higher than reported elsewhere. We found evidence of a significantly reduced survival in patients with neurolisteriosis treated with adjunctive dexamethasone, and also determined the time window for fetal losses. MONALISA provides important new data to improve management and predict outcome in listeriosis. FUNDING: Programme Hospitalier Recherche Clinique, Institut Pasteur, Inserm, French Public Health Agency.

Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, 2013-2015.

In 2013, an unusual increase in the number of Salmonella enterica serotype Paratyphi A (Salmonella Paratyphi A) infections was reported in patients in Phnom Penh, Cambodia, and in European, American and Japanese travellers returning from Cambodia. Epidemiological investigations did not identify a common source of exposure. To analyse the population structure and genetic diversity of these Salmonella Paratyphi A isolates, we used whole-genome sequencing on 65 isolates collected from 1999 to 2014: 55 from infections acquired in Cambodia and 10 from infections acquired in other countries in Asia, Africa and Europe. Short-read sequences from 80 published genomes from around the world and from 13 published genomes associated with an outbreak in China were also included. Pulsed-field gel electrophoresis (PFGE) was performed on a subset of isolates. Genomic analyses were found to provide much more accurate information for tracking the individual strains than PFGE. All but 2 of the 36 isolates acquired in Cambodia during 2013-2014 belonged to the same clade, C5, of lineage C. This clade has been isolated in Cambodia since at least 1999. The Chinese outbreak isolates belonged to a different clade (C4) and were resistant to nalidixic acid, whereas the Cambodian outbreak isolates displayed pan-susceptibility to antibiotics. Since 2014, the total number of cases has decreased, but there has been an increase in the frequency with which nalidixic acid-resistant C5 isolates are isolated. The frequency of these isolates should be monitored over time, because they display decreased susceptibility to ciprofloxacin, the first-choice antibiotic for treating paratyphoid fever.

Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes.

Listeria monocytogenes (Lm) is a major human foodborne pathogen. Numerous Lm outbreaks have been reported worldwide and associated with a high case fatality rate, reinforcing the need for strongly coordinated surveillance and outbreak control. We developed a universally applicable genome-wide strain genotyping approach and investigated the population diversity of Lm using 1,696 isolates from diverse sources and geographical locations. We define, with unprecedented precision, the population structure of Lm, demonstrate the occurrence of international circulation of strains and reveal the extent of heterogeneity in virulence and stress resistance genomic features among clinical and food isolates. Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is low (∼2.5 × 10-7 substitutions per site per year, as inferred from the core genome) and that major sublineages (corresponding to so-called 'epidemic clones') are estimated to be at least 50-150 years old. This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology.