Infectious diarrhoea contributes to high morbidity and mortality in young children from sub-Saharan Africa. The aim of this study was to assess the prevalence of single and multiple diarrhoeal-causing pathogen combinations in children suffering from diarrhoea from rural and peri-urban communities in South Africa. A total of 275 diarrhoea stool specimens were collected between 2014 and 2016 from Hospitals and Primary Health Care clinics. The BioFire^® FilmArray^® Gastrointestinal panel was used to simultaneously detect 22 diarrhoea pathogens (viruses, bacteria, parasites) known to cause diarrhoea. A total of 82% (226/275) enteric pathogens were detected in the stool specimens. The two most detected bacterial, viral and parasitic pathogens each included: EAEC (42%), EPEC (32%), Adenovirus F40/41 (19%), Norovirus (15%), Giardia (8%) and Cryptosporidium (6%), respectively. Single enteric pathogen infections were recorded in 24% (65/275) specimens with EAEC, and Norovirus was found in 26% (17/65) and 14% (9/65) of the specimens, respectively. Multiple enteric pathogen combinations were recorded in 59% (161/275) of the stool specimens with 53% (85/161) containing two pathogens, 22% (35/161) containing three pathogens and 25% (41/161) containing four or more pathogens. The results from this study demonstrated the complex nature of pathogen co-infections in diarrhoeal episodes which could have an impact on treatment effectiveness.

Diarrhoeagenic Escherichia coli pose a significant risk to human health. As such, determining the source(s) of these bacteria when isolated from patients with diarrhoea is an important step in disease prevention. To identify the presence of genes coding for virulence and phylogroups among E. coli isolated from children hospitalized due to diarrhoea in Limpopo Province, South Africa. E. coli isolates were identified using the VITEK-2 automated system. An 11-gene multiplex polymerase chain reaction (PCR) was used to differentiate five pathogenic types of E. coli: enteroaggregative (EAEC), enteroinvasive (EIEC), enterohaemorrhagic (EHEC), enteropathogenic (EPEC) and enterotoxigenic (ETEC). The Clermont quadruplex PCR method was used to identify phylogroups of isolates. From the 133 isolates tested, 79 were confirmed as E. coli. Of these, 19.0% (15/79) were commensals and 81.0% (64/79) were positive for at least one pathotype, of which ETEC was predominant (16.5%, 13/79), followed by EAEC (10.1%, 8/79), EPEC (7.6%, 6/79) and EHEC (2.5%, 2/79). Hybrid pathotypes were also detected and EAEC/ETEC was predominant (25.3%, 20/79). Phylogroup B2 was predominant (30.4%, 24/79), followed by phylogroup B1 (22.8%, 18/79), and phylogroups C and E (both 12.7%, 10/79). Just over 6% (5/79) of isolates were non-typable. There was a high distribution of diarrhoeagenic E. coli associated with different phylogroups among children living in Limpopo Province, South Africa. This emphasizes the importance of future monitoring of virulence and phylogroup distribution of E. coli isolates in this province in particular and in South Africa as a whole.

River water quality is an important health issue as the water is utilised for drinking, domestic and agricultural use in developing countries. This study aimed to investigate the effect water from a major city has on the water quality of the Jukskei River that daylights in Johannesburg, South Africa. The river water samples were analysed for physio-chemical properties, microbiology, antibiotic resistance of bacterial isolates, genetic markers, and potentially toxic metals. Data analysis revealed increased electrical conductivity, total dissolved solids, and turbidity since 2010. Total Coliform and Escherichia coli detected were above the South African water quality guidelines for domestic, recreational, and irrigation purposes. Additionally, sodium, zinc, nickel, lithium, and lead exceeded the guidelines in domestic, recreational, and irrigation water. Pathogenic strains of E. coli (aEPEC, EHEC, EIEC, and EAEC) were isolated from the water. Various other potentially pathogenic organisms that have been implicated as causes of gastro-intestinal, and a wide range of other diseases, were also detected and demonstrated multiple levels of resistance to antibiotics tested. The results show that the river water is a potential health threat to downstream users. These results will feed into the environmental management action plan for Water for the Future (NGO group).

Globally, millions of children die as a result of diarrhoea and/or antimicrobial resistant infections. Diarrhoeagenic Escherichia coli (DEC) are responsible for a substantial proportion of cases of diarrhoea in South Africa and sub-Saharan Africa. Effective treatments (including the use of antimicrobials) are therefore essential. E. coli isolated from children under the age of five were subjected to antimicrobial susceptibility testing using the Vitek 2® compact automated system (bioMérieux Inc., France) and categorized as multidrug or extensively drug resistant (MDR or XDR). Almost all isolates (164/166, 98.8 %) were categorized as MDR with 4.9 % (9/166) categorized as XDR. The majority of isolates (153/166, 92.2 %) were also phenotypically classified as extended-spectrum β-lactamase (ESBL) producers. More than half of these isolates (78/153, 51.0 %) were subjected to PCR for genes associated with ESBL production. More than half (45/78, 57.7 %) of the isolates tested were PCR positive for at least one ESBL gene or gene group and 11.5 % (9/78) were positive for two ESBL genes or gene groups. There is a need to strengthen antimicrobial resistance surveillance in South Africa and improve infection prevention and control measures. There is also a need to review the current South African Treatment Guidelines as outlined by the South African Essential Drugs Programme.

Background: Poor air quality contributes to the global burden of respiratory disease, with both bacteria and fungi contributing to the number of deaths associated with community‐ and healthcare‐associated infections, especially those caused by antimicrobial‐resistant microbes. Methods: During February and March of 2025, air samples were collected within a Johannesburg clinic directly onto Brilliance Escherichia coli /Coliform Selective, MacConkey Agar, and Potato Dextrose Agar (Oxoid, United Kingdom), which were incubated at 37°C and 32°C, respectively. Resulting bacterial isolates were identified and subjected to antimicrobial susceptibility testing using the Vitek 2 compact system (BioMérieux Inc., France), and unique fungal isolates were identified using polymerase chain reaction amplification of internal transcribed spacer regions and subsequent sequencing. Results: After identification, all but three fungal isolates were categorized as pathogens or opportunistic pathogens. All Gram‐negative ( n = 77; 100%) and almost all Gram‐positive ( n = 52/54; 96.30%) isolates were categorized as multidrug‐resistant. Significant proportions of both Gram‐negative and Gram‐positive isolates, including members of the ESKAPEE group of pathogens ( Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa , Enterobacter species, and E. coli ), were found to be resistant to antimicrobials used as first‐line treatments for respiratory and other infections and antimicrobials of last resort such as colistin and vancomycin. Conclusion: Almost all microbes identified and characterized in the present study pose a significant risk of infection and a source of spread of antimicrobial resistance. It is, therefore, recommended that the infection prevention and control program at the clinic in question be reviewed and that monitoring continue.

Background: Environmental surfaces are key reservoirs for pathogen transmission, with the survival of bacteria on fomites influenced by factors such as temperature, humidity, and microbial interactions. This study aimed to determine microbial surface contamination and to determine the antimicrobial resistance profile of bacteria isolated from the indoor surface where the presence of cockroaches was observed in households of the Greater Letaba Municipality (GLM), South Africa. Methods: Swab samples were collected from kitchen countertops and food storage areas with visible cockroach activity. Bacteria were isolated and identified using standard microbiological methods, and antimicrobial susceptibility testing (AST) was conducted with the Vitek^® Automated 2 system. Results: Of the 120 samples collected, 82 (68%) showed bacterial growth, resulting in 190 isolates. The majority of isolates (93%) were Gram-negative, comprising Klebsiella, Pseudomonas, Enterobacter, Escherichia, Serratia, Stenotrophomonas, Pantoea, Raoultella, and Salmonella species, with 98% demonstrating multidrug resistance (MDR) to multiple antibiotics. Resistance was particularly high against gentamicin (94%), fluoroquinolones (88%) and amikacin (77%). Among Gram-positive isolates, all belonged to the Enterococcus species, with 22% being resistant to one or two of the tested antimicrobial agents and 78% exhibiting MDR. Conclusions: The study revealed a high prevalence of antibiotic resistance in both Gram-positive and Gram-negative bacteria isolated from household surfaces. The spread of antibiotic-resistant pathogens via environmental surfaces presents a significant risk to human health, safety, and well-being.