Plugging the leaks: antibiotic resistance at human-animal interfaces in low-resource settings

Antibiotic resistance is one of the greatest public health challenges of our time. International efforts to curb resistance have largely focused on drug development and limiting unnecessary antibiotic use. However, in areas where water, sanitation, and hygiene infrastructure is lacking, we propose that bacterial flow between humans and animals can exacerbate the emergence and spread of resistant pathogens. Here, we describe the consequences of poor environmental controls by comparing mobile resistance elements among Escherichia coli recovered from humans and meat in Cambodia, a middle-income country with substantial human-animal connectivity and unregulated antibiotic use. We identified identical mobile resistance elements and a conserved transposon region that were widely dispersed in both humans and animals, a phenomenon rarely observed in high-income settings. Our findings indicate that plugging leaks at human-animal interfaces should be a critical part of addressing antibiotic resistance in low- and especially middle-income countries.

Prevalence and factors associated with faecal carriage of extended-spectrum β-lactamase-producing Enterobacterales among peripartum women in the community in Cambodia

Background

In Southeast-Asia, where many conditions associated with dissemination of ESBL-producing Enterobacterales (ESBL-E) in the community are met, data from the community are scarce but show high ESBL-E carriage prevalence. Maternal ESBL-E colonization is considered a risk factor for neonatal colonization, which is the first step towards developing neonatal sepsis. Despite this, ESBL-E carriage prevalence and its risk factors during pregnancy or postpartum remain undefined in Southeast-Asia.

Objectives

To estimate the prevalence of ESBL-E faecal colonization among peripartum women in the community of an urban and a rural area in Cambodia, to investigate ESBL-E genomic characteristics and to identify associated risk factors.

Methods

Epidemiological data and faecal samples from 423 peripartum women were collected in an urban and rural areas in Cambodia (2015–16). Bacterial cultures, antibiotic susceptibility tests and ESBL gene sequencing were performed. Risk factor analysis was conducted using logistic regression.

Results

The prevalence of ESBL-E faecal carriage was 79.2% (95% CI 75.0%–82.8%) among which Escherichia coli (n = 315/335, 94.0%) were most frequent. All isolates were multidrug resistant. Among 318 ESBL-E, the genes most frequently detected were bla_CTX-M-15 (41.5%), bla_CTX-M-55 (24.8%), and bla_CTX-M-27 (15.1%). Low income, undernutrition, multiparity, regular consumption of pork, dried meat, and raw vegetables, were associated with ESBL-E faecal carriage.

Conclusions

The high prevalence of ESBL-E carriage observed among peripartum women in Southeast-Asia and the identified associated factors underline the urgent need for public health measures to address antimicrobial resistance, including a ‘One Health’ approach.

CTX-M-55-type ESBL-producing Salmonella enterica are emerging among retail meats in Phnom Penh, Cambodia

Background

Salmonella enterica is a leading cause of human gastroenteritis. S. enterica strains that produce ESBLs (ESBL-Salm) remain rare in Europe and North America, but less is known about their prevalence among animal-derived foods in countries with weaker food safety practices and unregulated veterinary antibiotic use.

Objectives

To examine the prevalence and characteristics of ESBL-Salm from retail meats in Phnom Penh, Cambodia.

Methods

We tested fish, pork and chicken from two markets for ESBL- and carbapenemase-producing Salmonella from September-December 2016, using cefotaxime- and ertapenem-supplemented media, respectively. ESBL-Salm were sequenced and their genomes characterized. We performed plasmid conjugation experiments to assess the co-transferability of ESBL-encoding genes and MDR phenotypes.

Results

Twenty-six of 150 fish and meat samples (17%) were positive for ESBL-Salm, including 10/60 fish (17%), 15/60 pork (25%) and 1/30 chicken (3%). Carbapenemase-producing Salmonella strains were not detected. Pork-origin ESBL-Salm were primarily serotypes Rissen (10/15) or a monophasic variant of Typhimurium 4,5,12:i:- (3/15), whereas Saintpaul (3/10) and Newport (4/10) were more common among fish. Most ESBL enzymes were encoded by blaCTX-M-55 genes (24/26) harboured on conjugative IncA/C2 (n = 14) or IncHI2 (n = 10) plasmids. Resistance to up to six additional drug classes was co-transferred by each plasmid type. ESBL-Salm were resistant to almost every antibiotic recommended for severe salmonellosis treatment.

Conclusions

CTX-M-55-type S. enterica are highly prevalent among pork and fish from Phnom Penh markets and their spread appears to be mediated by MDR IncA/C2 and IncHI2 plasmids. Food safety must be improved and veterinary antibiotic use should be regulated to protect public health.

Meat and Fish as Sources of Extended-Spectrum β-Lactamase-Producing Escherichia coli, Cambodia

We compared extended-spectrum β-lactamase-producing Escherichia coli isolates from meat and fish, gut-colonized women, and infected patients in Cambodia. Nearly half of isolates from women were phylogenetically related to food-origin isolates; a subset had identical multilocus sequence types, extended-spectrum β-lactamase types, and antimicrobial resistance patterns. Eating sun-dried poultry may be an exposure route.

Paediatric haemolytic uraemic syndrome related to Shiga toxin-producing Escherichia coli, an overview of 10 years of surveillance in France, 2007 to 2016

IntroductionHaemolytic uraemic syndrome (HUS) related to Shiga toxin-producing Escherichia coli (STEC) is the leading cause of acute renal failure in young children. In France, HUS surveillance in children aged < 15 years was implemented starting from 1996.AimWe present the results of this surveillance between 2007 and 2016.MethodsA voluntary nationwide network of 32 paediatric departments notifies cases. Two national reference centres perform microbiological STEC confirmation.ResultsOver the study period, the paediatric HUS incidence rate (IR) was 1.0 per 100,000 children-years, with a median of 116 cases/year. In 2011, IR peaked at 1.3 per 100,000 children-years, and decreased to 1.0 per 100,000 children-years in 2016. STEC O157 associated HUS peaked at 37 cases in 2011 and decreased to seven cases in 2016. Cases of STEC O26-associated HUS have increased since 2010 and STEC O80 associated HUS has emerged since 2012, with 28 and 18 cases respectively reported in 2016. Four STEC-HUS food-borne outbreaks were detected (three STEC O157 linked to ground beef and raw-milk cheese and one STEC O104 linked to fenugreek sprouts). In addition, two outbreaks related to person-to-person transmission occurred in distinct kindergartens (STEC O111 and O26).ConclusionsNo major changes in HUS IRs were observed over the study period of 10 years. However, changes in the STEC serogroups over time and the outbreaks detected argue for continuing epidemiological and microbiological surveillance.

Enterohemorrhagic Escherichia coli Hybrid Pathotype O80:H2 as a New Therapeutic Challenge

This emerging clonal group harbors the extraintestinal virulence–associated plasmid pS88 and can induce invasive infections and death.

We describe the epidemiology, clinical features, and molecular characterization of enterohemorrhagic Escherichia coli (EHEC) infections caused by the singular hybrid pathotype O80:H2, and we examine the influence of antibiotics on Shiga toxin production. In France, during 2005–2014, a total of 54 patients were infected with EHEC O80:H2; 91% had hemolytic uremic syndrome. Two patients had invasive infections, and 2 died. All strains carried stx2 (variants stx2a, 2c, or 2d); the rare intimin gene (eae-ξ); and at least 4 genes characteristic of pS88, a plasmid associated with extraintestinal virulence. Similar strains were found in Spain. All isolates belonged to the same clonal group. At subinhibitory concentrations, azithromycin decreased Shiga toxin production significantly, ciprofloxacin increased it substantially, and ceftriaxone had no major effect. Antibiotic combinations that included azithromycin also were tested. EHEC O80:H2, which can induce hemolytic uremic syndrome complicated by bacteremia, is emerging in France. However, azithromycin might effectively combat these infections.

Travel- and Community-Based Transmission of Multidrug-Resistant Shigella sonnei Lineage among International Orthodox Jewish Communities

Shigellae are sensitive indicator species for studying trends in the international transmission of antimicrobial-resistant Enterobacteriaceae. Orthodox Jewish communities (OJCs) are a known risk group for shigellosis; Shigella sonnei is cyclically epidemic in OJCs in Israel, and sporadic outbreaks occur in OJCs elsewhere. We generated whole-genome sequences for 437 isolates of S. sonnei from OJCs and non-OJCs collected over 22 years in Europe (the United Kingdom, France, and Belgium), the United States, Canada, and Israel and analyzed these within a known global genomic context. Through phylogenetic and genomic analysis, we showed that strains from outbreaks in OJCs outside of Israel are distinct from strains in the general population and relate to a single multidrug-resistant sublineage of S. sonnei that prevails in Israel. Further Bayesian phylogenetic analysis showed that this strain emerged approximately 30 years ago, demonstrating the speed at which antimicrobial drug-resistant pathogens can spread widely through geographically dispersed, but internationally connected, communities.

Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease.

Recurrent Hemolytic and Uremic Syndrome Induced by Escherichia Coli

A widespread belief is that typical hemolytic and uremic syndrome (HUS) does not recur. We report the case of a patient infected twice with raw milk taken from his own cow and containing a Shiga toxin-producing Escherichia coli O174:H21 that induced recurrent HUS causing severe renal and cerebral disorders. A genomic comparison of the human and bovine Shiga toxin-producing Escherichia coli O174:H21 isolates revealed that they were identical. Typical HUS may recur. Since milk from this animal was occasionally distributed locally, thereby posing a serious threat for the whole village, this particular cow was destroyed.

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence.

Fatal case of hemolytic-uremic syndrome in an adult due to a rare serogroup O91 Entero hemorrhagic Escherichia coli associated with a Clostridium difficile infection. More than meets the eye

Hemolytic-uremic syndrome due to enterohemorrhagic Escherichia coli, belonging to serogroup O91 has rarely been described. We report here a case of post-diarrheal HUS due to EHEC O91 in an elderly patient for whom diagnosis was delayed given a previously diagnosed C. difficile infection. This case highlights the usefulness of Shiga-toxin detection.

Prevalence of Shiga toxin-producing Shigella species isolated from French travellers returning from the Caribbean: an emerging pathogen with international implications

Shiga toxins (Stxs) are potent cytotoxins that inhibit host cell protein synthesis, leading to cell death. Classically, these toxins are associated with intestinal infections due to Stx-producing Escherichia coli or Shigella dysenteriae serotype 1, and infections with these strains can lead to haemolytic-uraemic syndrome. Over the past decade, there has been increasing recognition that Stx is produced by additional Shigella species. We recently reported the presence and expression of stx genes in Shigella flexneri 2a clinical isolates. The toxin genes were carried by a new stx-encoding bacteriophage, and infection with these strains correlated with recent travel to Haiti or the Dominican Republic. In this study, we further explored the epidemiological link to this region by utilizing the French National Reference Centre for Escherichia coli, Shigella and Salmonella collection to survey the frequency of Stx-producing Shigella species isolated from French travellers returning from the Caribbean. Approximately 21% of the isolates tested were found to encode and produce Stx. These isolates included strains of S. flexneri 2a, S. flexneri Y, and S. dysenteriae 4. All of the travellers who were infected with Stx-producing Shigella had recently travelled to Haiti, the Dominican Republic, or French Guiana. Furthermore, whole genome sequencing showed that the toxin genes were encoded by a prophage that was highly identical to the phage that we identified in our previous study. These findings demonstrate that this new stx-encoding prophage is circulating within that geographical area, has spread to other continents, and is capable of spreading to multiple Shigella serogroups.

Shopper cards data and storage practices for the investigation of an outbreak of Shiga-toxin producing Escherichia coli O157 infections

INTRODUCTION

An outbreak of shiga-toxin producing Escherichia coli infections occurred in southwest France in June 2012. The outbreak was investigated to identify the source of infection, and guide control measures.

METHODS

Confirmed outbreak cases were patients who developed bloody diarrhoea or haemolytic uremic syndrome (HUS) between 28 May and 6 July 2012, with E. coli O157 isolates showing indistinguishable patterns on pulse field gel electrophoresis (PFGE). A standardized questionnaire was administered to patients to document food consumption and other risk exposures. Their purchase was checked through their supermarket shopper card data.

RESULTS

Six patients (four with HUS and two with bloody diarrhea) were confirmed outbreak cases. Fresh ground beef burgers from one supermarket were the only common food exposure, identified by interviews and shopper card data. The PFGE profile of shiga toxin-producing E. coli O157 isolated from the suspected beef burgers was identical to those from the human cases. The suspected beef burgers were no longer on sale at the time of investigation but three patients confirmed as outbreak cases had deep-frozen some at home.

CONCLUSION

Shopper card data was particularly useful to obtain precise and reliable information on the traceability of consumed food. Despite the expired use-by date, a recall was issued for the beef burgers. This contributed to preventing other cases among consumers who had deep-frozen the beef burgers.

[Enterohemorragic Escherichia coli (EHEC): topical enterobacteriaceae]

Since the 1980s, EnterohaemorrhagicEscherichia coli (EHEC) have been recognised as emergent pathogens causing foodborne outbreaks. The latest one is the E. coli O104:H4 outbreak which occurred in Germany in May 2011 then in France. In France, the surveillance of EHEC infections is based on surveillance of hemolytic-uremic syndrome (HUS) in children under 15 years old. The average annual incidence is 0.8/100,000 children under 15 years old with a predominance of the O157:H7 serotype. EHEC are one of the six clinical pathovars of E. coli defined by their capacity to produce Shiga-toxins and for that reason, are part of a larger group called: Shigatoxin-producingE. coli (STEC). EHEC are a cause of different troubles ranging from mild diarrhea to haemorrhagic colitis which might be complicated by HUS in young children and thrombocytopenic thrombotic purpura in adults. The reservoir of EHEC is mainly the intestinal tract of ruminants: EHEC are transmitted via ingestion of contaminated food or water, person-to-person contact, direct animal contact and exposure to the environment. The diagnosis of the EHEC infections relies on isolation of STEC in stool samples or detection of genes encoding for Shiga-toxins. Treatment is mainly symptomatic. Use of antibiotics is controversial because the risk of HUS could be increased (release of toxins).

Prevalence, quantification and antimicrobial resistance of Campylobacter spp. on chicken neck-skins at points of slaughter in 5 major cities located on 4 continents

Quantitative data on Campylobacter contamination of food are lacking, notably in developing countries. We assessed Campylobacter contamination of chicken neck-skins at points of slaughter in 5 major cities in Africa (Dakar in Senegal, Yaounde in Cameroon), Oceania (Noumea in New Caledonia), the Indian Ocean (Antananarivo in Madagascar) and Asia (Ho Chi Minh City (HCMC) in Vietnam. One hundred and fifty slaughtered chickens were collected in each of the 5 major cities from semi-industrial abattoirs or markets (direct slaughter by the seller), and 65.5% (491/750) were found to be Campylobacter-positive. Two cities, Yaounde and Noumea, demonstrated high prevalence Campylobacter detection rates (92.7% and 96.7% respectively) in contrast with HCMC (15.3%). Four species were identified among 633 isolates, namely C. jejuni (48.3%), C. coli (37.3%), C. lari (11.7%) and C. upsaliensis (1%). HCMC was the only city with C. lari isolation as was Antananarivo for C. upsaliensis. C. coli was highly prevalent only in Yaounde (69.5%). Among the 491 samples positive in Campylobacter detection, 329 were also positive with the enumeration method. The number of Campylobacter colony-forming units (CFU) per gram of neck-skin in samples positive in enumeration was high (mean of the log(10): 3.2 log(10) CFU/g, arithmetic mean: 7900CFU/g). All the cities showed close enumeration means except HCMC with a 1.81 log(10) CFU/g mean for positive samples. Semi-industrial abattoir was linked to a significant lower count of Campylobacter contamination than direct slaughter by the seller (p=0.006). On 546 isolates (546/633, 86.3%) tested for antibiotic susceptibility, resistance to erythromycin, ampicillin and ciprofloxacin was observed for respectively 11%, 19% and 50%. HCMC was the city where antibiotic resistant rates were the highest (95%, p=0.014). Considering the 329 positive chickens in Campylobacter enumeration, the mean number of resistant isolates to at least 2 different antibiotic families (19.8%), may be estimated ca. 1500CFU/g; the corresponding mean of the log(10) would be 2.5 log(10)CFU/g. As chickens are sold at slaughter and brought directly at home to be cooked, these data suggest a high probability of cross-contamination. A substantial proportion of isolates are drug-resistant, which could lead to potential public health issues. Health authorities should consider measures to reduce Campylobacter contamination of chicken during farming and at slaughter, and to provide appropriate food hygiene education. Further studies are needed in particular to investigate food-handling practices in domestic kitchens.

Outbreak of haemolytic uraemic syndrome due to Shiga toxin-producing Escherichia coli O104:H4 among French tourists returning from Turkey, September 2011

Eight cases of diarrhoea, including two cases of haemolytic uraemic syndrome (HUS), were identified among 22 French tourists who travelled to Turkey in September 2011. A strain of Escherichia coli O104:H4 stx2-positive, eae-negative, hlyA-negative, aggR-positive, ESBL-negative was isolated from one HUS case. Molecular analyses show this strain to be genetically similar but not indistinguishable from the E. coli O104:H4 2011 outbreak strain of France and Germany. Although the source of infection was not identified, we conclude that the HUS cases had probably been infected in Turkey.

Enteropathogenic Escherichia coli o157 in Bangui and N'Goila, Central African Republic: A brief report

Escherichia coli O157:H7 producing Shiga like toxins is a food-borne pathogen frequently isolated in Bangui from patients with hemorrhagic colitis (HC). This survey provides comprehensive data on the high prevalence of E. coli O157:H7 infection in Bangui: carriage of E. coli O157:H7 by zebu (Bos indicus) and fish, contamination of the fields at N'Goila where the butchers kill the zebus, and contamination of the field surface water along the M'Poko River upstream of the Oubangui River where fish are caught, appear to be important contributory factors. We also describe novel strains of serogroup O157:NM isolated from zebu and from fish; a variety of assays indicate that these strains belong to the enteropathogenic pathotype, though they lack certain genetic elements thought to be diagnostic for this pathotype.

Experimental validation of low virulence in field strains of Listeria monocytogenes

Several reports have described Listeria monocytogenes strains which were nonpathogenic or weakly pathogenic, but little is known about these low-virulence strains. We found that 9 field L. monocytogenes strains were hypovirulent and 17 were avirulent, based on the number of mice contaminated and the colonization of their spleens after subcutaneous inoculation. All these strains possessed the known virulence genes. We have now assessed the low virulence of these strains in other assays before determining how they differ from virulent strains. We have shown that the low-virulence strains exhibited a phenotypic stability and were not a mixture of virulent and avirulent bacteria. They did not recover virulence after many passages in mice and colonized the spleens of mice more poorly than virulent strains after i.v. inoculation. Their lethal capacities, determined by 50% lethal dose (LD(50)), were lower than those of virulent strains. Like Listeria innocua, 14 of 17 avirulent strains had no LD(50) and were eliminated by the lymph nodes after subcutaneous inoculation. The virulent, hypovirulent, and avirulent strains were always significantly different, whatever the tests of virulence used, confirming the importance of these low-virulence field strains in identifying the proteins involved in virulence.

Multicenter study of street foods in 13 towns on four continents by the food and environmental hygiene study group of the international network of pasteur and associated institutes

An international multicenter study of ready-to-eat foods, sandwiches, and ice creams or sorbets sold in the streets and their vendors was carried out to assess the microbiological quality of these foods and to identify characteristics of the vendors possibly associated with pathogens. Thirteen towns in Africa, America, Asia, and Oceania were involved in the study. A single protocol was used in all 13 centers: representative sampling was by random selection of vendors and a sample of foods bought from each of these vendors at a time and date selected at random. Microbiological analyses were carried out using standardized Association Française de Normalisation methods, and the use of a standardized questionnaire to collect data concerning the characteristics of the vendors. Fifteen surveys were carried out, with 3,003 food samples from 1,268 vendors. The proportion of unsatisfactory food samples was between 12.7 and 82.9% for ice creams and sorbets and between 11.3 and 92% for sandwiches. For ice creams and sorbets, the sale of a large number of units (>80 per day) increased the risk of unsatisfactory food by a factor of 2.8 (95% confidence interval [CI]: 1.5 to 5.1), lack of training in food hygiene by 6.6 (95% CI: 1.1 to 50). and by a factor of 2.8 (95% CI: 1.4 to 5.4) for mobile vendors. These risk factors were not identified for sandwiches, this difference may be due to the presence of a cooking step in their preparation. These results show that the poor microbiological quality of these street foods constitutes a potential hazard to public health, that the extent of this hazard varies between the cities studied, and that vendors' health education in food safety is a crucial factor in the prevention of foodborne infections.

Energetics of Intra- and Inter-molecular Bonds in the Three Nitrophenols

A thermodynamic study of the three nitrophenol isomers (general formula C6H5NO3) was realized by combustion calorimetry of small amounts of substance (a few milligrams), sublimation calorimetry, differential thermal analysis and heat capacity measurements. The experimental enthalpies of combustion, sublimation and fusion of these compounds are as follows: ortho para -ΔcH�m(s,298.15K)/kJ mol-1 2871.0�1.3 2875.1�0.9 2868.5�1.0 ΔsubH�m(298.15K)/kJ mol-1 72.30�0.28 91.23�0.49 92.39�0.43 ΔfusHm/kJ mol-1 18.32�0.35 20.54�0.34 17.33�0.10 Ttriple point/K 318.40�0.01 370.51�0.01 387.26�0.05   The strength of the intramolecular hydrogen bond in the ortho isomer was estimated equal to 20.09 kJ mol-1. The relative stability of the three isomers is discussed, and the intermolecular bond enthalpies have been determined. The experimental resonance energies Eexp,conj are 168.7, 142.8 and 148.2 kJ mol-1 for ortho -, meta- and para-nitrophenol respectively, and are in good agreement with theoretical values. The experimental atomization enthalpies Δa,expH°m(298.15K) are 6742.5�1.9, 6719.5�1.7 and 6724.9�1.8 kJ mol-1 for ortho -, meta- and para-nitrophenol respectively.