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

Antibiotic resistance of Escherichia coli isolated from food and clinical environment in China from 2001 to 2020

Antibiotics are widely used in China's aquaculture, agricultural, and clinical settings and can lead to antibiotic resistance in various pathogens. Although the pooled prevalence estimate (PPE) and antibiotic resistance of Escherichia coli (E. coli) in food and clinical settings has been extensively studied, a comprehensive analysis of the published literature is lacking. We conducted a comprehensive search for research indicators for 2001-2020 in eight major Chinese and English literature databases. Antibiotic PPE and resistance trends of 5933 and 29,451 E. coli isolates were screened and analysed in 35 food studies (total 1821) and 62 clinical studies (total 5159). E. coli strains derived from food had the highest antibiotic resistance rate to tetracycline (TET, 71.3 %), followed by trimethoprim-sulfamethoxazole (SXT, 62.5 %) and cefazolin (CFZ, 36.2 %). E. coli strains isolated from clinical environments were highly resistant to piperacillin (PIP, 71.7 %), TET (68.3 %) and CFZ (60.9 %), consistent with foodborne E. coli drug resistance patterns. E. coli strains isolated from food and clinical samples collected in laboratories carry multiple antibiotic resistance genes (ARGs), such as blaTEM, gryA, gryB, sul1, and tetA, making E. coli a reservoir of ARGs. This study highlights the presence of drug-resistant E. coli pathogens and ARGs in food and clinical environments.

Effects of breastfeeding on children's gut colonization with multidrug-resistant Enterobacterales in peri-urban Lima, Peru

Children living in low-resource settings are frequently gut-colonized with multidrug-resistant bacteria. We explored whether breastfeeding may protect against children's incident gut colonization with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) and Klebsiella, Enterobacter, or Citrobacter spp. (ESBL-KEC). We screened 937 monthly stool samples collected from 112 children aged 1-16 months during a 2016-19 prospective cohort study of enteric infections in peri-urban Lima. We used 52,816 daily surveys to examine how exposures to breastfeeding in the 30 days prior to a stool sample were associated with children's risks of incident gut-colonization, controlling for antibiotic use and other covariates. We sequenced 78 ESBL-Ec from 47 children to explore their diversity. Gut-colonization with ESBL-Ec was increasingly prevalent as children aged, approaching 75% by 16 months, while ESBL-KEC prevalence fluctuated between 18% and 36%. Through 6 months of age, exclusively providing human milk in the 30 days prior to a stool sample did not reduce children's risk of incident gut-colonization with ESBL-Ec or ESBL-KEC. From 6 to 16 months of age, every 3 additional days of breastfeeding in the prior 30 days was associated with 6% lower risk of incident ESBL-Ec gut-colonization (95% CI: 0.90, 0.98, p = .003). No effects were observed on incident ESBL-KEC colonization. We detected highly diverse ESBL-Ec among children and few differences between children who were predominantly breastfed (mean age: 4.1 months) versus older children (10.8 months). Continued breastfeeding after 6 months conferred protection against children's incident gut colonization with ESBL-Ec in this setting. Policies supporting continued breastfeeding should be considered in efforts to combat antibiotic resistance.

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.

Extended Spectrum β-Lactamase-Producing Enterobacterales of Shrimp and Salmon Available for Purchase by Consumers in Canada-A Risk Profile Using the Codex Framework

The extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-EB) encompass several important human pathogens and are found on the World Health Organization (WHO) priority pathogens list of antibiotic-resistant bacteria. They are a group of organisms which demonstrate resistance to third-generation cephalosporins (3GC) and their presence has been documented worldwide, including in aquaculture and the aquatic environment. This risk profile was developed following the Codex Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance with the objectives of describing the current state of knowledge of ESBL-EB in relation to retail shrimp and salmon available to consumers in Canada, the primary aquacultured species consumed in Canada. The risk profile found that Enterobacterales and ESBL-EB have been found in multiple aquatic environments, as well as multiple host species and production levels. Although the information available did not permit the conclusion as to whether there is a human health risk related to ESBLs in Enterobacterales in salmon and shrimp available for consumption by Canadians, ESBL-EB in imported seafood available at the retail level in Canada have been found. Surveillance activities to detect ESBL-EB in seafood are needed; salmon and shrimp could be used in initial surveillance activities, representing domestic and imported products.

Zoonotic sources and the spread of antimicrobial resistance from the perspective of low and middle-income countries

BACKGROUND

Antimicrobial resistance is an increasing challenge in low and middle-income countries as it is widespread in these countries and is linked to an increased mortality. Apart from human and environmental factors, animal-related drivers of antimicrobial resistance in low- and middle-income countries have special features that differ from high-income countries. The aim of this narrative review is to address the zoonotic sources and the spread of antimicrobial resistance from the perspective of low- and middle-income countries.

MAIN BODY

Contamination with extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is highest in poultry (Africa: 8.9-60%, Asia: 53-93%) and there is a risk to import ESBL-producing E. coli through poultry meat in Africa. In aquacultures, the proportion of ESBL-producers among E. coli can be high (27%) but the overall low quality of published studies limit the general conclusion on the impact of aquacultures on human health. ESBL-producing E. coli colonization of wildlife is 1-9% in bats or 2.5-63% birds. Since most of them are migratory animals, they can disperse antimicrobial resistant bacteria over large distances. So-called 'filth flies' are a relevant vector not only of enteric pathogens but also of antimicrobial resistant bacteria in settings where sanitary systems are poor. In Africa, up to 72.5% of 'filth flies' are colonized with ESBL-producing E. coli, mostly conferred by CTX-M (24.4-100%). While methicillin-resistant Staphylococcus aureus plays a minor role in livestock in Africa, it is frequently found in South America in poultry (27%) or pork (37.5-56.5%) but less common in Asia (poultry: 3%, pork: 1-16%).

CONCLUSIONS

Interventions to contain the spread of AMR should be tailored to the needs of low- and middle-income countries. These comprise capacity building of diagnostic facilities, surveillance, infection prevention and control in small-scale farming.

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.

Transmission routes of antibiotic resistant bacteria: a systematic review

Background

Quantification of acquisition routes of antibiotic resistant bacteria (ARB) is pivotal for understanding transmission dynamics and designing cost-effective interventions. Different methods have been used to quantify the importance of transmission routes, such as relative risks, odds ratios (OR), genomic comparisons and basic reproduction numbers. We systematically reviewed reported estimates on acquisition routes’ contributions of ARB in humans, animals, water and the environment and assessed the methods used to quantify the importance of transmission routes.

Methods

PubMed and EMBASE were searched, resulting in 6054 articles published up until January 1st, 2019. Full text screening was performed on 525 articles and 277 are included.

Results

We extracted 718 estimates with S. aureus (n = 273), E. coli (n = 157) and Enterobacteriaceae (n = 99) being studied most frequently. Most estimates were derived from statistical methods (n = 560), mainly expressed as risks (n = 246) and ORs (n = 239), followed by genetic comparisons (n = 85), modelling (n = 62) and dosage of ARB ingested (n = 17). Transmission routes analysed most frequently were occupational exposure (n = 157), travelling (n = 110) and contacts with carriers (n = 83). Studies were mostly performed in the United States (n = 142), the Netherlands (n = 87) and Germany (n = 60). Comparison of methods was not possible as studies using different methods to estimate the same route were lacking. Due to study heterogeneity not all estimates by the same method could be pooled.

Conclusion

Despite an abundance of published data the relative importance of transmission routes of ARB has not been accurately quantified. Links between exposure and acquisition are often present, but the frequency of exposure is missing, which disables estimation of transmission routes’ importance. To create effective policies reducing ARB, estimates of transmission should be weighed by the frequency of exposure occurrence.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07360-z.

Understanding how food safety risk perception influences dietary decision making among women in Phenom Phnom Penh, Cambodia: a qualitative study

OBJECTIVES

To determine women's perception of the risk of food safety and how it relates to diet, health and decision making as part of formative research for a market-based intervention that aims to improve the safety of animal-source foods sold in informal markets.

DESIGN

Qualitative study including in-depth personal interviews with 24 caregivers were conducted and complemented with a second follow-up PhotoVoice interview, which allowed the women to photograph their meals and perceptions of food safety and nutrition. Interview data were analysed using thematic analysis in MAXQDA. Participants were purposively sampled from a larger Safe Food, Fair Food for Cambodia study, conducted from May to August 2018.

SETTING

Urban and periurban neighborhoods of Phnom Penh, Cambodia.

PARTICIPANTS

24 female caregivers (mothers and grandmothers) of children under age 5, each interviewed twice.

FINDINGS

A primary food safety concern expressed was that chemicals (pesticides and other agricultural additives) in animal-source foods, fruits and vegetables may impact the health of their families by causing diarrhoea and problems during pregnancy. This fear created a lack of trust in markets, which influenced their food purchasing behaviours and strategies for making the food safer for their families. These mitigation strategies, including food selection and cleaning, vary among the women but are perceived as important to be able to provide their families with what they define as safe meals.

CONCLUSIONS

Interventions that wish to decrease rates of foodborne illness and increase animal source food consumption should also address the belief that the food system has been compromised by the addition of pesticides and agricultural additives.

Epidemiology of extended-spectrum β-lactamase–producing Enterobacterales in five US sites participating in the Emerging Infections Program, 2017

Objective

The incidence of infections from extended-spectrum β-lactamase (ESBL)–producing Enterobacterales (ESBL-E) is increasing in the United States. We describe the epidemiology of ESBL-E at 5 Emerging Infections Program (EIP) sites.

Methods

During October–December 2017, we piloted active laboratory- and population-based (New York, New Mexico, Tennessee) or sentinel (Colorado, Georgia) ESBL-E surveillance. An incident case was the first isolation from normally sterile body sites or urine of Escherichia coli or Klebsiella pneumoniae/oxytoca resistant to ≥1 extended-spectrum cephalosporin and nonresistant to all carbapenems tested at a clinical laboratory from a surveillance area resident in a 30-day period. Demographic and clinical data were obtained from medical records. The Centers for Disease Control and Prevention (CDC) performed reference antimicrobial susceptibility testing and whole-genome sequencing on a convenience sample of case isolates.

Results

We identified 884 incident cases. The estimated annual incidence in sites conducting population-based surveillance was 199.7 per 100,000 population. Overall, 800 isolates (96%) were from urine, and 790 (89%) were E. coli. Also, 393 cases (47%) were community-associated. Among 136 isolates (15%) tested at the CDC, 122 (90%) met the surveillance definition phenotype; 114 (93%) of 122 were shown to be ESBL producers by clavulanate testing. In total, 111 (97%) of confirmed ESBL producers harbored a blaCTX-M gene. Among ESBL-producing E. coli isolates, 52 (54%) were ST131; 44% of these cases were community associated.

Conclusions

The burden of ESBL-E was high across surveillance sites, with nearly half of cases acquired in the community. EIP has implemented ongoing ESBL-E surveillance to inform prevention efforts, particularly in the community and to watch for the emergence of new ESBL-E strains.

Antibiotic Use and Resistance Knowledge Assessment of Personnel on Chicken Farms with High Levels of Antimicrobial Resistance: A Cross-Sectional Survey in Ica, Peru

Poultry farming represents Peru’s primary food animal production industry, where antimicrobial growth promoters are still commonly used, exerting selective pressure on intestinal microbial populations. Consumption and direct animal-to-human transmission have been reported, and farmworkers are at high risk of colonization with resistant bacteria. We conducted a cross-sectional survey among 54 farmworkers to understand their current antimicrobial resistance (AMR) awareness in Ica, Peru. To gain insight into the potential work-related risk of exposure to bacteria, we also measured the AMR rates in Escherichia coli isolated among 50 broiler chickens. Farmworkers were unaware of antimicrobial resistance (31.5%) or antibiotic resistance (16.7%) terms. Almost two-thirds (61%) consumed antibiotics during the previous month, and only 42.6% received a prescription from a healthcare professional. A total of 107 E. coli chicken isolates were obtained, showing a high frequency of multidrug-resistant (89.7%) and extended-spectrum beta-lactamase (ESBL) production (71.9%). Among ESBL-producer isolates, 84.4% carried the bla_CTX-M gene. Results identified gaps in knowledge that reflect the need for interventions to increase antimicrobial awareness among poultry farmworkers. The high AMR rates among E. coli isolates highlight the need to reduce antimicrobial use in poultry farms. Our findings reveal a critical need for effective policy development and antimicrobial stewardship interventions in poultry production in Ica, Peru.

OUP accepted manuscript

Background

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) is a major cause of infections worldwide. An understanding of the reservoirs and modes of transmission of these pathogens is essential, to tackle their increasing frequency.

Objectives

We investigated the contributions of various compartments (humans, animals, environment), to human colonization or infection with ESBL-Ec over a 3 year period, on an island.

Methods

The study was performed on Reunion Island (Southwest Indian Ocean). We collected ESBL-Ec isolates prospectively from humans, wastewater and livestock between April 2015 and December 2018. Human specimens were recovered from a regional surveillance system representative of the island’s health facilities. These isolates were compared with those from livestock and urban/rural wastewater, by whole-genome sequencing.

Results

We collected 410 ESBL-Ec isolates: 161 from humans, 161 from wastewater and 88 from animals. Phylogenomic analysis demonstrated high diversity (100 STs), with different STs predominating among isolates from humans (ST131, ST38, ST10) and animals (ST57, ST156). The large majority (90%) of the STs, including ST131, were principally associated with a single compartment. The CTX-M-15, CTX-M-27 and CTX-M-14 enzymes were most common in humans/human wastewater, whereas CTX-M-1 predominated in animals. Isolates of human and animal origin had different plasmids carrying bla_CTX-M genes, with the exception of a conserved IncI1-ST3 bla_CTX-M-1 plasmid.

Conclusions

These molecular data suggest that, despite their high level of contamination, animals are not a major source of the ESBL-Ec found in humans living on this densely populated high-income island. Public health policies should therefore focus primarily on human-to-human transmission, to prevent human infections with ESBL-Ec.

Market Chickens as a Source of Antibiotic-Resistant Escherichia coli in a Peri-Urban Community in Lima, Peru

The widespread and poorly regulated use of antibiotics in animal production in low- and middle-income countries (LMICs) is increasingly associated with the emergence and dissemination of antibiotic resistance genes (ARGs) in retail animal products. Here, we compared Escherichia coli from chickens and humans with varying levels of exposure to chicken meat in a low-income community in the southern outskirts of Lima, Peru. We hypothesize that current practices in local poultry production result in highly resistant commensal bacteria in chickens that can potentially colonize the human gut. E. coli was isolated from cloacal swabs of non-organic (n = 41) and organic chickens (n = 20), as well as from stools of market chicken vendors (n = 23), non-vendors (n = 48), and babies (n = 60). 315 E. coli isolates from humans (n = 150) and chickens (n = 165) were identified, with chickens showing higher rates of multidrug-resistant and extended-spectrum beta-lactamase phenotypes. Non-organic chicken isolates were more resistant to most antibiotics tested than human isolates, while organic chicken isolates were susceptible to most antibiotics. Whole-genome sequencing of 118 isolates identified shared phylogroups between human and animal populations and 604 ARG hits across genomes. Resistance to florfenicol (an antibiotic commonly used as a growth promoter in poultry but not approved for human use) was higher in chicken vendors compared to other human groups. Isolates from non-organic chickens contained genes conferring resistance to clinically relevant antibiotics, including mcr-1 for colistin resistance, blaCTX-M ESBLs, and blaKPC-3 carbapenemase. Our findings suggest that E. coli strains from market chickens are a potential source of ARGs that can be transmitted to human commensals.

The use of multi-pronged screening strategy to understand the epidemiology of carbapenemase-producing Enterobacteriaceae in Hong Kong: transition from epidemic to endemic setting

A multi-pronged carbapenemase-producing Enterobacteriaceae (CPE) screening strategy was implemented in Hong Kong West healthcare network. Of 199,192 fecal specimens from 77,194 patients screening from 1 July 2011 to 30 June 2019, the incidence of CPE per 1000 patient admission significantly increased from 0.01 (2012) to 1.9 (2018) (p<0.01). With appropriate infection control measures, the incidence of nosocomial CPE per 1000 CPE colonization day decreased from 22.34 (2014) to 10.65 (2018) (p=0.0094). Exposure to wet market for purchasing raw pork (p=0.007), beef (p=0.017), chicken (p=0.026), and vegetable (p=0.034) for >3 times per week significantly associated with community acquisition of CPE. Strategic CPE control measures should be implemented in both the hospital and the community.

Prevalence of MDR organism (MDRO) carriage in children and their household members in Siem Reap Province, Cambodia

BACKGROUND

The rising incidence of infections caused by MDR organisms (MDROs) poses a significant public health threat. However, little has been reported regarding community MDRO carriage in low- and middle-income countries.

METHODS

We conducted a cross-sectional study in Siem Reap, Cambodia comparing hospital-associated households, in which an index child (age: 2-14 years) had been hospitalized for at least 48 h in the preceding 2-4 weeks, with matched community households on the same street, in which no other child had a recent history of hospitalization. Participants were interviewed using a survey questionnaire and tested for carriage of MRSA, ESBL-producing Enterobacterales (ESBL-E) and carbapenemase-producing Enterobacterales (CPE) by culture followed by antibiotic susceptibility testing. We used logistic regression analysis to analyse associations between collected variables and MDRO carriage.

RESULTS

Forty-two pairs of households including 376 participants with 376 nasal swabs and 290 stool specimens were included in final analysis. MRSA was isolated from 26 specimens (6.9%). ESBL-producing Escherichia coli was detected in 269 specimens (92.8%) whereas ESBL-producing Klebsiella pneumoniae was isolated from 128 specimens (44.1%), of which 123 (42.4%) were co-colonized with ESBL-producing E. coli. Six (2.1%) specimens tested positive for CPE (4 E. coli and 2 K. pneumoniae). The prevalence ratios for MRSA, ESBL-producing E. coli and ESBL-producing K. pneumoniae carriage did not differ significantly in hospital-associated households and hospitalized children compared with their counterparts.

CONCLUSIONS

The high prevalence of ESBL-E across both household types suggests that MDRO reservoirs are common in the community. Ongoing genomic analyses will help to understand the epidemiology and course of MDRO spread.

On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference

Recently developed MinHash-based techniques were proven successful in quickly estimating the level of similarity between large nucleotide sequences. This article discusses their usage and limitations in practice to approximating uncorrected distances between genomes, and transforming these pairwise dissimilarities into proper evolutionary distances. It is notably shown that complex distance measures can be easily approximated using simple transformation formulae based on few parameters. MinHash-based techniques can therefore be very useful for implementing fast yet accurate alignment-free phylogenetic reconstruction procedures from large sets of genomes. This last point of view is assessed with a simulation study using a dedicated bioinformatics tool.

High Prevalence of Multiple Antibiotic-Resistant, Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli in Fresh Seafood Sold in Retail Markets of Mumbai, India

In this study, fresh seafood in retail markets was investigated for the antibiotic susceptibility patterns of the faecal indicator Escherichia coli and distribution of important β-lactamase encoding genes. E. coli were isolated from 50 (37 fish and 13 shellfish) fresh seafood samples and studied with respect to the phenotypic and genotypic characters of antibiotic resistance. Of 475 E. coli isolates from fresh seafood, 71.58% exhibited extended-spectrum β-lactamase (ESBL)-positive phenotypes. A high percentage of isolates were resistant to indicator cephalosporins cefotaxime (95%), cefpodoxime (90.88%) and ceftazidime (90.29%). Relatively higher susceptibilities were recorded against imipenem (74.41%), cefoxitin (66.76%) and meropenem (51.18%). The multiple antibiotic resistance (MAR) index of 97.35% of the isolates was above 0.18. The ESBL genes bla_CTX-M, bla_SHV and bla_TEM were detected in 62.37%, 23.35% and 2.6% of E. coli isolates, respectively. The ESBL-producing isolates also harboured the metallo-β-lactamase-encoding genes bla_OXA (7.06%), bla_NDM (4.42%) and bla_VIM (0.88%). This study highlights the risk of dissemination of multidrug resistant E. coli in seafood consumer communities and also the need to improve the hygiene of the coastal waters, landing centres and the retail markets.

A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies

This paper describes a novel alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences using publicly available bioinformatics tools. For each pair of genomes, a dissimilarity measure is first computed and next transformed to obtain an estimation of the number of substitution events that have occurred during their evolution. These pairwise evolutionary distances are then used to infer a phylogenetic tree and assess a confidence support for each internal branch. Analyses of both simulated and real genome datasets show that this bioinformatics procedure allows accurate phylogenetic trees to be reconstructed with fast running times, especially when launched on multiple threads. Implemented in a publicly available script, named JolyTree, this procedure is a useful approach for quickly inferring species trees without the burden and potential biases of multiple sequence alignments.

Escherichia coli ST410 among humans and the environment in Southeast Asia

Escherichia coli ST410 (Ec-ST410) is an emerging, multidrug-resistant clone. Recent investigations of its global epidemiology and evolution have been based almost exclusively on isolates from Europe and North America. It is unclear whether Southeast Asian-origin Ec-ST410 (SEA-Ec-ST410) belong to these same clones or represent regionally disseminated variants. Antimicrobial resistance mechanisms among SEA-Ec-ST410 were characterised, and whether they belonged to regional variants was investigated by contextualising them within a global collection. Seven Ec-ST410 were identified among a recent collection of expanded-spectrum cephalosporin-resistant E. coli recovered from 91 healthy women (stool) and 26 infected patients (blood and urine) living in Phnom Penh, Cambodia. Nine additional Ec-ST410 genomes were identified from Thailand (n = 7) and Vietnam (n = 2) through EnteroBase and PubMed searches. The assembled genomes were characterised and a SNP-based phylogenetic tree was created comparing these 16 SEA-Ec-ST410 with a previously published Ec-ST410 collection, primarily sourced from Europe (97/128) and North America (24/128). SEA-Ec-ST410 belonged to several distinct branches within previously described clonal clades. SEA-Ec-ST410 within the B3/H24Rx sublineage encoded bla_CTX-M-55 (8/12) and F18:A-:B1 plasmid replicons (6/12), neither of which were detected among other Ec-ST410 belonging to this clade. Three of four SEA-Ec-ST410 within the B4/H24RxC sublineage lacked both bla_OXA-181 and an IncX3 plasmid replicon that were harboured by 97% and 100% of all other Ec-ST410 in this sublineage (n = 64), respectively. In conclusion, Ec-ST410 are present in Southeast Asia following multiple introductions. The unique pattern of antimicrobial resistance elements harboured by SEA-Ec-ST410 suggests independent circulation in the region.

Antimicrobial resistance in Cambodia: a review

OBJECTIVES

Following the launch of the Global Antimicrobial Resistance Surveillance System (GLASS), antimicrobial resistance (AMR) rates in many countries remain poorly described. This review provides an overview of published AMR data from Cambodia in the context of recently initiated national human and food-animal surveillance.

METHODS

PubMed and the Cochrane Database of Systematic Reviews were searched for articles published from 2000 to 2018, which reported antimicrobial susceptibility testing (AST) data for GLASS specific organisms isolated from Cambodia. Articles were screened using strict inclusion/exclusion criteria. AST data was extracted, with medians and ranges of resistance rates calculated for specific bug-drug combinations.

RESULTS

Twenty-four papers were included for final analysis, with 20 describing isolates from human populations. Escherichia coli was the most commonly described organism, with median resistance rates from human isolates of 92.8% (n=6 articles), 46.4% (n=4), 55.4% (n=8), and 46.4% (n=5) to ampicillin, 3^rd generation cephalosporins, fluoroquinolones, and gentamicin respectively.

CONCLUSIONS

Whilst resistance rates are high for several GLASS organisms, there were insufficient data to draw robust conclusions about the AMR situation in Cambodia. The recently implemented national AMR surveillance systems will begin to address this data gap.