Co-detection of virulent Escherichia coli genes in surface water sources

Overview of pathogenic Escherichia coli, with a focus on Shiga toxin-producing serotypes, global outbreaks (1982-2024) and food safety criteria

Classification of pathogenic E. coli has been focused either in mammalian host or infection site, which offers limited resolution. This review presents a comprehensive framework for classifying all E. coli branches within a single, unifying figure. This approach integrates established methods based on virulence factors, serotypes and clinical syndromes, offering a more nuanced and informative perspective on E. coli pathogenicity. The presence of the LEE island in pathogenic E. coli is a key genetic marker differentiating EHEC from STEC strains. The coexistence of stx and eae genes within the bacterial genome is a primary characteristic used to distinguish STEC from other pathogenic E. coli strains. The presence of the inv plasmid, Afa/Dr adhesins, CFA-CS-LT-ST and EAST1 are key distinguishing features for identifying pathogenic E. coli strains belonging to EIEC, DAEC, ETEC and EAEC pathotypes respectively. Food microbiological criteria differentiate pathogenic E. coli in food matrices. 'Zero-tolerance' applies to most ready-to-eat (RTE) foods due to high illness risk. Non-RTE foods' roles may allow limited E. coli presence, which expose consumers to potential risk; particularly from the concerning Shiga toxin-producing E. coli (STEC) strains, which can lead to life-threatening complications in humans, including haemolytic uremic syndrome (HUS) and even death in susceptible individuals. These findings suggest that decision-makers should consider incorporating the separate detection of STEC serotypes into food microbiological criteria, in addition to existing enumeration methods. Contamination of STEC is mainly linked to food consumption, therefore, outbreaks of E. coli STEC has been reviewed here and showed a link also to water as a potential contamination route. Since their discovery in 1982, over 39,787 STEC cases associated with 1,343 outbreaks have been documented. The majority of these outbreaks occurred in the Americas, followed by Europe, Asia and Africa. The most common serotypes identified among the outbreaks were O157, the 'Big Six' (O26, O45, O103, O111, O121, and O145), and other serotypes such as O55, O80, O101, O104, O116, O165, O174 and O183. This review provides valuable insights into the most prevalent serotypes implicated in STEC outbreaks and identifies gaps in microbiological criteria, particularly for E. coli non-O157 and non-Big Six serotypes.

Antimicrobial Resistance Linked to Septic System Contamination in the Indiana Lake Michigan Watershed

Extended-spectrum β-lactamases confer resistance to a variety of β-lactam antimicrobials, and the genes for these enzymes are often found on plasmids that include additional antimicrobial resistance genes (ARG). We surveyed aquatic environments in the Indiana Lake Michigan watershed in proximity to areas with high densities of residential septic systems to determine if human fecal contamination from septic effluent correlated with the presence of antimicrobial resistance genes and phenotypically resistant bacteria. Of the 269 E. coli isolated from environmental samples and one septic source, 97 isolates were resistant to cefotaxime, a third-generation cephalosporin. A subset of those isolates showed phenotypic resistance to other β-lactams, fluoroquinolones, sulfonamides, and tetracyclines. Quantitative PCR was used to quantify human-associated Bacteroides dorei gene copies (Human Bacteroides) from water samples and to identify the presence of ARG harbored on plasmids from E. coli isolates or in environmental DNA. We found a strong correlation between the presence of ARG and human fecal concentrations, which supports our hypothesis that septic effluent is a source of ARG and resistant organisms. The observed plasmid-based resistance adds an additional level of risk, as human-associated bacteria from septic systems may expand the environmental resistome by acting as a reservoir of transmissible resistance genes.

Prevalence and Molecular Characterisation of Extended-Spectrum Beta-Lactamase-Producing Shiga Toxin-Producing Escherichia coli, from Cattle Farm to Aquatic Environments

Extended-spectrum beta-lactamase (ESBL)-producing bacteria are a major problem for public health worldwide because of limited treatment options. Currently, only limited information is available on ESBL-producing Shiga toxin-producing Escherichia coli (STEC) in cattle farms and the surrounding aquatic environment. This study sought to track and characterise ESBL-producing STEC disseminating from a cattle farm into the water environment. Animal husbandry soil (HS), animal manure (AM), animal drinking water (ADW), and nearby river water (NRW) samples were collected from the cattle farm. Presumptive ESBL-producing STEC were isolated and identified using chromogenic media and mass spectrophotometry methods (MALDI-TOF-MS), respectively. The isolates were subjected to molecular analysis, and all confirmed ESBL-producing STEC isolates were serotyped for their O serogroups and assessed for antibiotic resistance genes (ARGs) and for the presence of selected virulence factors (VFs). A phylogenetic tree based on the multilocus sequences was constructed to determine the relatedness among isolates of ESBL-producing STEC. The highest prevalence of ESBL-producing STEC of 83.33% was observed in HS, followed by ADW with 75%, NRW with 68.75%, and the lowest was observed in AM with 64.58%. Out of 40 randomly selected isolates, 88% (n = 35) belonged to the serogroup O45 and 13% (n = 5) to the serogroup O145. The multilocus sequence typing (MLST) analysis revealed four different sequence types (STs), namely ST10, ST23, ST165, and ST117, and the predominant ST was found to be ST10. All 40 isolates carried sul1 (100%), while bla_OXA, bla_CTX-M, sul2, bla_TEM, and qnrS genes were found in 98%, 93%, 90%, 83%, and 23% of the 40 isolates, respectively. For VFs, only stx2 was detected in ESBL-producing STEC isolates. The results of the present study indicated that a cattle environment is a potential reservoir of ESBL-producing STEC, which may disseminate into the aquatic environment through agricultural runoff, thus polluting water sources. Therefore, continual surveillance of ESBL-producing STEC non-O157 would be beneficial for controlling and preventing STEC-related illnesses originating from livestock environments.

Genetic characterization and antimicrobial susceptibility of Escherichia coli isolated from household water sources in northern Ghana

The microbial quality of household water is an important issue in developing countries, especially in Ghana, where many people still depend on unimproved sources of water. The present study investigated the prevalence, genetic characteristics, and antimicrobial resistance profile of Escherichia coli from surface water sources. Fifty-two water samples were analyzed by using a spread plate, a biochemical test, and multiplex polymerase chain reactions. E. coli was isolated from each of the 52 water samples. Of these isolates, 75% were noted to possess virulence genes. Approximately 54% of the isolates were characterized as follows: enterotoxigenic E. coli (ETEC, 10.26%), enteropathogenic E. coli (EPEC, 17.95%), verotoxigenic E. coli (VTEC, 23.07%), and enteroinvasive E. coli (EIEC, 2.57%). Eighteen of the fifty-two isolates could not be characterized due to heterogeneity in banding. The disc diffusion method was used to test for antimicrobial susceptibility. The isolates were most resistant to ceftazidime, augmentin, and cefuroxime. Multidrug resistance was recorded in 48.1% of the isolates. In contrast, the isolates were most susceptible to ciprofloxacin (86.5%), nitrofurantoin (84.6%), and ofloxacin (75%). These results revealed a high diversity and widespread of E. coli in northern Ghana. The study provides important data for public health nationwide surveillance of E. coli in surface water across the country.

Community monitoring of coliform pollution in Lake Tanganyika

Conventional water quality monitoring has been done for decades in Lake Tanganyika, under different national and international programs. However, these projects utilized monitoring approaches, which were temporally limited, labour intensive and costly. This study examines the use of citizen science to monitor the dynamics of coliform concentrations in Lake Tanganyika as a complementary method to statutory and project-focused measurements. Persons in five coastal communities (Kibirizi, Ilagala, Karago, Ujiji and Gombe) were trained and monitored total coliforms, faecal coliforms and turbidity for one year on a monthly basis, in parallel with professional scientists. A standardized and calibrated Secchi tube was used at the same time to determine turbidity. Results indicate that total and faecal coliform concentrations determined by citizen scientists correlated well to those determined by professional scientists. Furthermore, citizen scientist-based turbidity values were shown to provide a potential indicator for high FC and TC concentrations. As a simple tiered approach to identify increased coliform loads, trained local citizen scientists could use low-cost turbidity measurements with follow up sampling and analysis for coliforms, to inform their communities and regulatory bodies of high risk conditions, as well as to validate local mitigation actions. By comparing the spatial and temporal dynamics of coliform concentrations to local conditions of infrastructure, population, precipitation and hydrology in the 15 sites (3 sites per community) over 12 months, potential drivers of coliform pollution in these communities were identified, largely related to precipitation dynamics and the land use.

Occurrence of Hybrid Diarrhoeagenic Escherichia coli Associated with Multidrug Resistance in Environmental Water, Johannesburg, South Africa

This study was undertaken to determine the virulence and antibiotic resistance profiles of diarrhoeagenic Escherichia coli (DEC) in environmental waters of Johannesburg, South Africa. Samples were collected and cultured on selective media. An 11-plex PCR assay was used to differentiate five DEC, namely: enteroaggregative (EAEC), enterohaemorrhagic (EHEC), enteroinvasive (EIEC), enteropathogenic (EPEC) and enterotoxigenic (ETEC). The antibiotic resistance profile of isolates was determined using the VITEK®-2 automated system. The virulence profiles of 170 E. coli tested showed that 40% (68/170) were commensals and 60% (102/170) were pathogenic. EPEC had a prevalence of 19.2% (32/170), followed by ETEC 11.4% (19/170), EAEC 6% (10/170) and EHEC 3% (5/170). Hybrid DEC carrying a combination of simultaneously two and three pathogenic types was detected in twenty-eight and nine isolates, respectively. The antibiotic susceptibility testing showed isolates with multidrug resistance, including cefuroxime (100%), ceftazidime (86%), cefotaxime (81%) and cefepime (79%). This study highlighted the widespread occurrence of DEC and antibiotic resistance strains in the aquatic ecosystem of Johannesburg. The presence of hybrid pathotypes detected in this study is alarming and might lead to more severe diseases. There is a necessity to enhance surveillance in reducing the propagation of pathogenic and antibiotic-resistant strains in this area.

Carriage of colistin-resistant Gram-negative bacteria in children from communities in Cape Town (Tuberculosis child multidrug-resistant preventive therapy trial sub-study)

Colistin is a last-resort antibiotic against multidrug-resistant, Gram-negative bacteria. Colistin resistance has been described in the clinical settings in South Africa. However, information on carriage of these bacteria in communities is limited. This study investigated gastrointestinal carriage of colistin-resistant Escherichia coli and Klebsiella spp. and mcr genes in children from communities in Cape Town. Colistin-resistant E. coli was isolated from two participants (4%, 2/50), and mcr-1-mcr-9 genes were not detected. Gastrointestinal carriage of colistin-resistant Enterobacterales was rare; however, continuous extensive surveillance is necessary to determine the extent of carriage and its contribution to resistance observed in clinical settings.

Characterisation of mobile colistin resistance genes (mcr-3 and mcr-5) in river and storm water in regions of the Western Cape of South Africa

Background

Colistin is regarded as a last-resort antimicrobial against multi-drug resistant Gram-negative bacteria (GNB), therefore the dissemination of colistin resistance in the environment is of great concern. Horizontal transfer of mobile colistin resistance (mcr) genes to potential pathogens poses a serious problem. This study aimed to describe the presence of colistin resistant GNB and mcr genes in river and storm water in regions of the Western Cape.

Methods

Water samples were collected from three rivers during May 2019 and January 2020 and two storm water samples were collected in November 2019. Colistin resistant GNB were cultured on MacConkey agar containing colistin and identified by MALDI-TOF. Colistin resistance was confirmed using broth microdilution (BMD). mcr-1-5 genes were detected by PCR performed directly on the water samples and on the colistin resistant isolates. mcr functionality was assessed by BMD after cloning the mcr genes into pET-48b(+) and expression in SHuffle T7 E. coli.

Results

mcr-5.1 and various mcr-3 gene variants were detected in the Plankenburg-, Eerste- and Berg rivers and in storm water from Muizenberg, and only mcr-5.1 was detected in storm water from Fish Hoek. Colistin resistant GNB were isolated from all of the water sources. Aeromonas spp. were the most common colistin resistant organisms detected in the water sources; 25% (6/24) of colistin resistant Aeromonas spp. isolated from the Berg river contained novel mcr-3 variants; mcr-3.33 (n = 1), mcr-3.34 (n = 1) mcr-3.35 (n = 1) mcr-3.36 (n = 2) and mcr-3.37 (n = 1), which were confirmed to confer colistin resistance.

Conclusions

The mcr-5.1 and mcr-3 colistin resistance gene variants were present in widely dispersed water sources in regions of the Western Cape. The mcr genes were only detected in water sampled downstream of and alongside communities, suggesting that their presence is driven by human influence/contamination. This is the first documentation of mcr-3 and mcr-5 gene variants in any setting in South Africa. Spill-over of these genes to communities could result in horizontal gene transfer to pathogenic bacteria, exacerbating the challenge of controlling multidrug resistant GNB infections.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-021-00963-2.

Characterisation of mcr-4.3 in a colistin-resistant Acinetobacter nosocomialis clinical isolate from Cape Town, South Africa

OBJECTIVES

Colistin resistance in Acinetobacter spp. is increasing, resulting in potentially untreatable nosocomial infections. Plasmid-mediated colistin resistance is of particular concern due to its low fitness cost and potential transferability to other bacterial strains and species. This study investigated the colistin resistance mechanism in a clinical Acinetobacter nosocomialis isolate from Cape Town, South Africa.

METHODS

A colistin-resistant A. nosocomialis isolate was identified from a blood culture in 2017. PCR and Illumina whole-genome sequencing (WGS) were performed to identify genes and mutations conferring resistance to colistin. Plasmid sequencing was performed on an Oxford Nanopore platform. mcr functionality was assessed by broth microdilution after cloning the mcr gene into pET-48b(+) and expressing it in SHuffle® T7 Escherichia coli and after curing the plasmid using 62.5 mg/L acridine orange.

RESULTS

The colistin minimum inhibitory concentration (MIC) of the A. nosocomialis isolate was 16 mg/L. The mcr-4.3 gene was detected by PCR and WGS. No other previously described colistin resistance mechanism was found by WGS. The mcr-4.3 gene was identified on a 24 024-bp RepB plasmid (pCAC13a). Functionality studies showed that recombinant mcr-4.3 did not confer colistin resistance in E. coli. However, plasmid curing of pCAC13a restored colistin susceptibility in A. nosocomialis.

CONCLUSION

We describe the first detection of a plasmid-mediated mcr-4.3 gene encoding colistin resistance in A. nosocomialis and the first detection of mcr-4.3 in a clinical isolate in Africa. Recombinant expression of mcr-4.3 did not confer colistin resistance in E. coli, suggesting that its functionality may be RepB plasmid-dependent or species-specific.

Detection of Shiga toxin-encoding genes in small community water supplies

Shiga toxin (Stx), one of the most potent bacterial toxins known, can cause bloody diarrhea, hemolytic uremic syndrome, kidney failure and death. The aim of this pilot was to investigate the occurrence of Shiga toxin-encoding genes, stx (stx1 and stx2) from total coliform (TC) and E. coli positive samples from small community water systems. After aliquots for TC and E. coli analyses were removed, the remnant volume of the samples was enriched, following a protocol developed for this study. Fifty-two per cent of the samples tested by multiplex PCR were positive for the presence of the stx genes; this percentage was higher in raw water samples. The stx2 gene was more abundant. Testing larger volumes of the samples increase the sensitivity of our assay, providing an alternative protocol for the detection of Shiga toxin-producing E. coli (STEC) that might be missed by the TC assay. This study confirms the presence of Stx encoding genes in source and distributed water for all systems sampled and suggests STEC as a potential health risk in small systems.

Development of three multiplex-PCR assays for virulence profiling of different iron acquisition systems in Escherichia coli

BACKGROUND AND OBJECTIVES

Escherichia coli is responsible for various enteric and extraintestinal infections in animals and humans. Iron as an essential nutrient, has a proven role in pathogenicity of E. coli. Pathogenic E. coli benefits of having complicated systems for iron acquisition but our current knowledge is limited because of complexity of these systems. In the present study, three multiplex-PCR assays were developed to screen nine different virulence genes related to diverse iron acquisition systems in E. coli.

MATERIALS AND METHODS

The multiplex-PCR systems were designed and optimized in three panels. Each panel includes a triplex-PCR cocktail. The panels are as follow: panel 1: iroN, iutA and fecA; panel 2: fyuA, sitA and irp2; and panel 3: iucD, chuA and tonB. A total of 39 pathogenic E. coli was screened according to the designed multiplex-PCR.

RESULTS

In total, the top three frequent genes were tonB (100%), fecA (66.6%) and sitA (58.9%). With the exception of fecA and tonB, comparing the prevalence of genes among different origin of isolates (human, cattle, poultry and pigeon) showed significant associations (P < 0.05). Moreover, the iroN, sitA and iucD genes were significantly prevalent (P < 0.05) among members of extraintestinal pathogenic E. coli in comparison with the group of diarrheagenic E. coli.

CONCLUSION

The current multiplex-PCR assays could be a valuable, rapid and economic tool to investigate diverse iron acquisition systems in E. coli for more precise virulence typing of pathogenic or commensal strains.

Determination of the Microbial and Chemical Loads in Rivers from the Quito Capital Province of Ecuador (Pichincha)-A Preliminary Analysis of Microbial and Chemical Quality of the Main Rivers

Contamination of natural water sources is one of the main health problems worldwide, which could be caused by chemicals, metals, or microbial agents. This study aimed to analyze the quality of 18 rivers located in Quito, the capital province of Pichincha, Ecuador, through physico-chemical and microbial parameters. The E. coli and total coliforms assessments were performed by a counting procedure in growth media. Polymerase chain reaction (PCR) was realized to detect several microbial genera, as well as Candida albicans, two parasites (Cryptosporidium and Giardia spp.) and E. coli pathotypes: enterohemorrhagic E. coli (EHEC), enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC) and enteropathogenic E. coli (EPEC). Additionally, physico-chemical parameters and major and trace metals were analyzed in each surface water sample. Our results demonstrated that most of the rivers analyzed do not comply with the microbial, physico-chemical, and metal requirements established by the Ecuadorian legislation. In terms of microbial pollution, the most polluted rivers were Monjas, Machángara, Pisque, and Pita Rivers. Furthermore, three out of four analyzed E. coli pathotypes (EIEC, EHEC, and EAEC) were detected in certain rivers, specifically: Monjas River showed the presence of EIEC and EHEC; in the Machángara River, EAEC and EIEC were detected; and finally, EIEC was present in the Guayllabamba River. Several physico-chemical parameters, such as pH, CODtotal, and TSS values, were higher than the Ecuadorian guidelines in 11, 28, and 28% of the rivers, respectively. Regarding heavy metals, Zn, Cu, Ni, Pb, Cd, and Mn surpassed the established values in 94, 89, 61, 22, 22, and 17% of the rivers, respectively. Machangara River was the only one that registered higher Cr concentrations than the national guidelines. The values of Al and Fe were above the recommended values in 83 and 72% of the rivers. Overall, based on the physical-chemical and microbiological parameters the most contaminated rivers were Machángara and Monjas. This study revealed severe contaminations in Ecuadorean Rivers; further studies should evaluate the sources of contamination and their impact on public health.

Multi-Drug-Resistant Diarrheagenic Escherichia coli Pathotypes in Pediatric Patients with Gastroenteritis from Central Iran

Background

Diarrheagenic Escherichia coli (DEC) is a significant cause of gastroenteritis and a major public health problem. This study investigates the prevalence and the antibiotic resistance patterns of DEC that were isolated from infectious diarrhea samples of pediatric patients from central Iran.

Patients and Methods

Pediatric diarrhea samples were collected from 230 pediatric patients visiting the hospital. E. coli pathotypes were diagnosed by using conventional culture methods and PCR. Antibiotic resistance profiles, the frequency of multi-drug resistance (MDR), and the phenotypic and genotypic characteristics of extended spectrum-β-lactamase (ESBL), AmpC and integron-associated genes were analyzed.

Results

Of the 230 samples of infectious diarrhea, 91 (39.5%) produced E. coli isolates. Of these, 32 cases (35.1%) were identified as DEC by culture and PCR. The frequency of the E. coli pathotypes obtained was as follows: EAEC 11/32 (34.3%), EPEC 9/32 (28.1%), ETEC 6/32 (18.7%), EIEC 3/32 (9.3%), and EHEC 3/32 (9.3%). The antibiotic resistance rates were greater for nalidixic acid (30/32; 93.7%), ampicillin (29/32; 90.6%), and tetracycline (25/32; 78.1%) than for any of the other tested antibiotics. High levels of MDR (25/32; 78.1%) and the presence of ESBL (18/32; 56.2%) and AmpC (9/32; 28.1%) were observed in the DEC isolates. The isolates showed a higher frequency of the ESBL genes [bla_TEM (18/18; 100%), bla_CTX-M15 (17/18; 94.4%)], and AmpC [bla _CIT (4/9; 44.4%) and bla_DHA (4/9; 44.4%)] than of the other ESBL and AmpC genes.

Conclusion

Compared to the previous study, DEC appeared to be the second-most abundant agent of diarrhea in pediatric patients after Campylobacter jejuni, with frequent MDR and ESBL presence.

Exploring the antimicrobial resistance profiles of WHO critical priority list bacterial strains

BACKGROUND

The antimicrobial resistance of clinical, environmental and control strains of the WHO "Priority 1: Critical group" organisms, Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa to various classes of antibiotics, colistin and surfactin (biosurfactant) was determined.

METHODS

Acinetobacter baumannii was isolated from environmental samples and antibiotic resistance profiling was performed to classify the test organisms [A. baumannii (n = 6), P. aeruginosa (n = 5), E. coli (n = 7) and K. pneumoniae (n = 7)] as multidrug resistant (MDR) or extreme drug resistant (XDR). All the bacterial isolates (n = 25) were screened for colistin resistance and the mobilised colistin resistance (mcr) genes. Biosurfactants produced by Bacillus amyloliquefaciens ST34 were solvent extracted and characterised using ultra-performance liquid chromatography (UPLC) coupled to electrospray ionisation mass spectrometry (ESI-MS). The susceptibility of strains, exhibiting antibiotic and colistin resistance, to the crude surfactin extract (cell-free supernatant) was then determined.

RESULTS

Antibiotic resistance profiling classified four A. baumannii (67%), one K. pneumoniae (15%) and one P. aeruginosa (20%) isolate as XDR, with one E. coli (15%) and three K. pneumoniae (43%) strains classified as MDR. Many of the isolates [A. baumannii (25%), E. coli (80%), K. pneumoniae (100%) and P. aeruginosa (100%)] exhibited colistin resistance [minimum inhibitory concentrations (MICs) ≥ 4 mg/L]; however, only one E. coli strain isolated from a clinical environment harboured the mcr-1 gene. UPLC-MS analysis then indicated that the B. amyloliquefaciens ST34 produced C13-16 surfactin analogues, which were identified as Srf1 to Srf5. The crude surfactin extract (10.00 mg/mL) retained antimicrobial activity (100%) against the MDR, XDR and colistin resistant A. baumannii, P. aeruginosa, E. coli and K. pneumoniae strains.

CONCLUSION

Clinical, environmental and control strains of A. baumannii, P. aeruginosa, E. coli and K. pneumoniae exhibiting MDR and XDR profiles and colistin resistance, were susceptible to surfactin analogues, confirming that this lipopeptide shows promise for application in clinical settings.

Prevalence and antibiotic susceptibility patterns of enteric bacterial pathogens in human and non-human sources in an urban informal settlement in Cape Town, South Africa

Background

In light of rampant childhood diarrhoea, this study investigated bacterial pathogens from human and non-human sources in an urban informal settlement.

Meat from informal abattoirs (n = 85), river water (n = 64), and diarrheic stool (n = 66) were collected between September 2015 and May 2016. A duplex real-time PCR, gel-based PCR, and CHROMagar™STEC were used to screen Tryptic Soy Broth (TSB) for diarrheic E. coli. Standard methods were used to screen for other selected food and waterborne bacterial pathogens.

Results

Pathogens isolated from stool, meat, and surface water included Salmonella enterica (6, 5, 0%), Plesiomonas shigelloides (9, 0, 17%), Aeromonas sobria (3, 3, 0%), Campylobacter jejuni (5, 5, 0%), Shigella flexneri (17, 5, 0%), Vibrio vulnificus (0, 0, 9%), and diarrheic E. coli (21, 3, 7%) respectively. All the isolates were resistant to trimethoprim–sulphamethoxazole.

Conclusions

There was a high burden of drug resistant diarrheal pathogens in the stool, surface water and meat from informal slaughter. Integrated control measures are needed to ensure food safety and to prevent the spread of drug resistant pathogens in similar settings.

Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes

Freshwater environments are susceptible to possible contamination by residual antibiotics that are released through different sources, such as agricultural runoffs, sewage discharges and leaching from nearby farms. Freshwater environment can thus become reservoirs where an antibiotic impact microorganisms, and is an important public health concern. Degradation and dilution processes are fundamental for predicting the actual risk of antibiotic resistance dissemination from freshwater reservoirs. This study reviews major approaches for detecting and quantifying antibiotic resistance bacteria (ARBs) and genes (ARGs) in freshwater and their prevalence in these environments. Finally, the role of dilution, degradation, transmission and the persistence and fate of ARB/ARG in these environments are also reviewed. Culture-based single strain approaches and molecular techniques that include polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR) and metagenomics are techniques for quantifying ARB and ARGs in freshwater environments. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria), followed by lakes (up to 77% of the total detected bacteria), compared to dam, pond, and spring (<1%). Of most concern is the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE), which cause highly epidemic infections. Dilution and natural degradation do not completely eradicate ARBs and ARGs in the freshwater environment. Even if the ARBs in freshwater are effectively inactivated by sunlight, their ARG-containing DNA can still be intact and capable of transferring resistance to non-resistant strains. Antibiotic resistance persists and is preserved in freshwater bodies polluted with high concentrations of antibiotics. Direct transmission of indigenous freshwater ARBs to humans as well as their transitory insertion in the microbiota can occur. These findings are disturbing especially for people that rely on freshwater resources for drinking, crop irrigation, and food in form of fish.

Risk of acquisition of human diarrhoeagenic Escherichia coli virulence genes in intercontinental travellers: A prospective, multi-centre study

BACKGROUND

We studied geographic distribution of diarrhoeagenic Escherichia coli virulence genes (DEC VGs) acquisition in travellers and investigated if they acquired highly virulent EAEC/STEC hybrid strains.

METHODS

From the prospective, multicentre COMBAT study among 2001 Dutch travellers, 491 travellers were selected based on travel destination to 7 subregions. Faecal samples taken directly before and after travel were screened for nine DEC VGs with real-time PCR. Incidence proportions and rates were calculated for each gene and subregion.

RESULTS

479 travellers were analysed. 21.8% acquired aggR (EAEC), with highest acquisition rates in Northern and Western Africa and 15.3% acquired eae (STEC/EPEC) with highest rates in travellers to Western and Eastern Africa. ETEC (elt or est gene) was acquired by 4.2% of travellers and acquisition of est was associated with traveller's diarrhoea. Overall, the risk of acquiring DEC VGs was low in Southern Africa and South America. Although the combination of aggR (EAEC) and stx1/2 (STEC) was acquired by 3 travellers, these genes could not be detected together in a single E. coli strain.

CONCLUSIONS

The risk of acquisition of DEC VGs strongly depends on the travel destination, with those travelling to Africa - except Southern Africa - having a higher risk.

Prevalencia de genes de virulencia de Escherichia coli en aguas superficiales del Río Bravo en la ciudad de Reynosa, Tamaulipas

El objetivo de este trabajo fue determinar la presencia de genes de virulencia en cepas de E. coli aisladas del Río Bravo en la ciudad de Reynosa Tamaulipas. Mediante la técnica de PCR se realizó la detección de los genes que codifican para factores de virulencia como son eae, bfp, stx1 y stx2 en muestras de aguas superficiales del Río Bravo en el municipio de Reynosa Tamaulipas y se identificó que el gen stx2 (27%) fue el más prevalente, seguido de stx1 (10%). Aunque el resto de las muestras fueron consideradas comensales al no tener ninguno de los genes propuestos, la presencia de genes stx1 y stx2 son considerados como un riesgo a la población que tiene contacto con el agua superficial del Río Bravo, por lo cual es necesario un monitoreo microbiológico en esta zona.

Quantitative Risk Assessment of Hemolytic Uremic Syndrome Associated with Consumption of Bulk Milk Sold Directly from Producer to Consumer in South Africa

This study was conducted to estimate the hemolytic uremic syndrome (HUS) risk associated with consumption of producer-distributor bulk milk (PDBM) contaminated with Shiga toxin-producing Escherichia coli (STEC) in South Africa. Data were obtained from recently completed studies in South Africa taking into account prior collected prevalence data of STEC in raw and pasteurized PDBM and survey information from producer-distributor outlets and households. Inputs for the models were complemented with data from published and unpublished literature. A probabilistic exposure model was developed with Monte Carlo simulation in Excel add-in software using @Risk software. Hazard characterization was based on an exponential dose-response model to calculate the probability of illness from STEC infection in individuals 5 years and younger and individuals older than 5 years. The estimated mean STEC level was 0.12 CFU/mL (95% confidence interval [CI]: 0 to 1.2; σ = 0.34) for raw PDBM and 0.08 CFU/mL (95% CI: 0 to 1; σ = 0.27) for pasteurized PDBM. A higher risk of HUS cases per year was recorded in raw than in pasteurized PDBM and also in individuals younger than 5 years of age. For every 100,000 servings consumed, the expected median numbers of HUS cases per year from raw PDBM were 52 for 5 years and younger and 3.2 for older than 5 years. The median numbers of cases per year for pasteurized PDBM were 47 for 5 years and younger and 2.9 for older than 5 years. Sensitivity analysis revealed that serving volume and time taken to sell PDBM at producer-distributor outlets were the factors with the greatest impact on probability of illness. The models developed in this study are an example of risk assessments for milk produced and marketed from similar scenarios across the globe.

Prevalence of Virulence Genes Associated with Diarrheagenic Pathotypes of Escherichia coli Isolates from Water, Sediment, Fish, and Crab in Aby Lagoon, Côte d'Ivoire

This study was conducted to characterize virulence genes of Escherichia coli isolates from water, sediment, fish, and crab in Aby Lagoon. Serogrouping was performed by EPEC antisera in 113 E. coli strains. The presence of diarrhea-associated genes (eae, stx, AggR, elt, and est) was assessed by multiplex PCR using specific primers. Based on the multiplex PCR, sixty-two isolates (42 from water, 19 from sediment, and 1 from crab) were positive for virulence genes, including 34 positive for elt (ETEC), 46 positive for est (ETEC), 24 positive for both elt and est, 6 positive for stx (EHEC), 1 positive for both stx + est, and 1 positive for both stx + elt. Genes eae (EPEC) and AggR (EAEC) were not detected. Nine serogroups (O114, O127, O55, O111, O86, O119, O126, O128, and O142) were identified. This study revealed the presence of diarrheagenic and nondiarrheagenic E. coli and potential public health risks if fishery products are not appropriately cooked.

Molecular detection of Acanthamoeba spp., Naegleria fowleri and Vermamoeba (Hartmannella) vermiformis as vectors for Legionella spp. in untreated and solar pasteurized harvested rainwater

Background

Legionella spp. employ multiple strategies to adapt to stressful environments including the proliferation in protective biofilms and the ability to form associations with free-living amoeba (FLA). The aim of the current study was to identify Legionella spp., Acanthamoeba spp., Vermamoeba (Hartmannella) vermiformis and Naegleria fowleri that persist in a harvested rainwater and solar pasteurization treatment system.

Methods

Pasteurized (45 °C, 65 °C, 68 °C, 74 °C, 84 °C and 93 °C) and unpasteurized tank water samples were screened for Legionella spp. and the heterotrophic plate count was enumerated. Additionally, ethidium monoazide quantitative polymerase chain reaction (EMA-qPCR) was utilized for the quantification of viable Legionella spp., Acanthamoeba spp., V. vermiformis and N. fowleri in pasteurized (68 °C, 74 °C, 84 °C and 93 °C) and unpasteurized tank water samples, respectively.

Results

Of the 82 Legionella spp. isolated from unpasteurized tank water samples, Legionella longbeachae (35 %) was the most frequently isolated, followed by Legionella norrlandica (27 %) and Legionella rowbothamii (4 %). Additionally, a positive correlation was recorded between the heterotrophic plate count vs. the number of Legionella spp. detected (ρ = 0.710, P = 0.048) and the heterotrophic plate count vs. the number of Legionella spp. isolated (ρ = 0.779, P = 0.0028) from the tank water samples collected. Solar pasteurization was effective in reducing the gene copies of viable V. vermiformis (3-log) and N. fowleri (5-log) to below the lower limit of detection at temperatures of 68–93 °C and 74–93 °C, respectively. Conversely, while the gene copies of viable Legionella and Acanthamoeba were significantly reduced by 2-logs (P = 0.0024) and 1-log (P = 0.0015) overall, respectively, both organisms were still detected after pasteurization at 93 °C.

Conclusions

Results from this study indicate that Acanthamoeba spp. primarily acts as the vector and aids in the survival of Legionella spp. in the solar pasteurized rainwater as both organisms were detected and were viable at high temperatures (68–93 °C).

Tracking bacterial virulence: global modulators as indicators

The genomes of Gram-negative bacteria encode paralogues and/or orthologues of global modulators. The nucleoid-associated H-NS and Hha proteins are an example: several enterobacteria such as Escherichia coli or Salmonella harbor H-NS, Hha and their corresponding paralogues, StpA and YdgT proteins, respectively. Remarkably, the genome of the pathogenic enteroaggregative E. coli strain 042 encodes, in addition to the hha and ydgT genes, two additional hha paralogues, hha2 and hha3. We show in this report that there exists a strong correlation between the presence of these paralogues and the virulence phenotype of several E. coli strains. hha2 and hha3 predominate in some groups of intestinal pathogenic E. coli strains (enteroaggregative and shiga toxin-producing isolates), as well as in the widely distributed extraintestinal ST131 isolates. Because of the relationship between the presence of hha2/hha3 and some virulence factors, we have been able to provide evidence for Hha2/Hha3 modulating the expression of the antigen 43 pathogenic determinants. We show that tracking global modulators or their paralogues/orthologues can be a new strategy to identify bacterial pathogenic clones and propose PCR amplification of hha2 and hha3 as a virulence indicator in environmental and clinical E. coli isolates.

Distribution and diversity of biosurfactant-producing bacteria in a wastewater treatment plant

The distribution and diversity of culturable biosurfactant-producing bacteria were investigated in a wastewater treatment plant (WWTP) using the Shannon and Simpson's indices. Twenty wastewater samples were analysed, and from 667 isolates obtained, 32 were classified as biosurfactant producers as they reduced the surface tension of the culture medium (71.1 mN/m), with the lowest value of 32.1 mN/m observed. Certain isolates also formed stable emulsions with diesel, kerosene and mineral oils. The 16S ribosomal RNA (rRNA) analysis classified the biosurfactant producers into the Aeromonadaceae, Bacillaceae, Enterobacteriaceae, Gordoniaceae and the Pseudomonadaceae families. In addition, numerous isolates carried the surfactin 4'-phosphopantetheinyl transferase (sfp), rhamnosyltransferase subunit B (rhlB) and bacillomycin C (bamC) genes involved in the biosynthesis of surfactin, rhamnolipid and bacillomycin, respectively. While, biosurfactant-producing bacteria were found at all sampling points in the WWTP, the Simpson's diversity (1 - D) and the Shannon-Weaver (H) indices revealed an increase in bacterial diversity in the influent samples (0.8356 and 2.08), followed by the effluent (0.8 and 1.6094) and then the biological trickling filter (0.7901 and 1.6770) samples. Numerous biosurfactant-producing bacteria belonging to diverse genera are thus present throughout a WWTP.