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A fifth of blood cultures from patients with infections acquired in a healthcare setting in South Africa will yield an organism. Carbapenem-resistant Enterobacterales (CREs), specifically Klebsiella pneumoniae are the most predominant Gram-negative bacteria (GNB) isolated among bloodstream infections (BSI). Additionally, the multidrug-resistant nature of these organisms is not only a threat to patients but it also poses a big public health challenge to current treatments and highlights the need for the development of new antimicrobials. Therefore, CRE have been placed on the critical priority list by the World Health Organization (WHO). We aimed to provide a holistic overview of the GERMS-SA CRE BSI surveillance data from 01 July 2015-31 December 2021. We conducted a cross-sectional study. CRE BSI was defined as the isolation of Enterobacterales resistant to any carbapenem (imipenem, ertapenem, meropenem and doripenem). All culture-confirmed cases captured on the database from 01 July 2015-31 December 2021 were considered for descriptive analysis and all cases with additional clinical information from 01 July 2015-31 December 2020 collected through the case report form (CRF) were used to perform analytical inferential statistics. We calculated the case fatality ratio of all cases with the outcome reported. Of the 5,258 culture-confirmed cases in the database for the surveillance period, the median age was 31 years (interquartile range 11-50) and 53.0% (2,787/5,258) were males. The majority of cases (64.6%, 1,361/2,017) were from Gauteng province that are participating in GERMS-SA surveillance. Of the cultures that isolated organisms, 53.0% (2,699/5,258) were sent to a reference laboratory for further testing. Case report forms were collected from 2,935 cases and these included audit cases. The clinical outcome was recorded for 99.5% (2,919/2,935) of the cases with a case fatality ratio of 36.1% (1,055/2,919). About 44.5% (1,298/2,916) of the cases had pre-existing conditions, most of which were other (n = 601). Most cases (78.4%, 2,288/2,920) received antibiotics on the current admission and 85.4% (2,488/2,912) had devices inserted. Of the 2,699 viable isolates, 2,100 (78%) were confirmed to be resistant to any of the carbapenems and 93.0% (n = 1,951) were carbapenemase-producing CREs. The carbapenem-resistant rate of all BSI was 1.9% (5,258/270,239). Of the CRE isolates, most were highly susceptible to fosfomycin (80.4%, 1,688/2,100). The potential significant risk factors for CRE BSI related mortality from multivariable logistic regression were being male, over 60 years, with pre-existing conditions, previously on antibiotics, mechanical ventilation as well as oxygenation, and previous hospital admission. Periodic surveillance for CRE should be performed on regular basis to support infection prevention and stewardship program at each facility.

After an increase in carbapenem-resistant Klebsiella pneumoniae (CRKP) bloodstream infections and associated deaths in the neonatal unit of a South Africa hospital, we conducted an outbreak investigation during October 2019-February 2020 and cross-sectional follow-up during March 2020-May 2021. We used genomic and epidemiologic data to reconstruct transmission networks of outbreak-related clones. We documented 31 cases of culture-confirmed CRKP infection and 14 deaths. Two outbreak-related clones (bla sequence type [ST] 152 [n = 16] and bla ST307 [n = 6]) cocirculated. The major clone bla ST152 accounted for 9/14 (64%) deaths. Transmission network analysis identified possible index cases of bla ST307 in October 2019 and bla ST152 in November 2019. During the follow-up period, 11 new cases of CRKP infection were diagnosed; we did not perform genomic analysis. Sustained infection prevention and control measures, adequate staffing, adhering to bed occupancy limits, and antimicrobial stewardship are key interventions to control such outbreaks.

Staphylococcus aureus is a healthcare-associated pathogen that can harbour multiple antimicrobial resistance determinants and express multiple virulence factors e.g. Panton-Valentine Leukocidin (PVL). Unknown staphylococcal cassette chromosome mec (SCCmec) typing patterns were previously observed among 11% (n = 52) of methicillin-resistant S. aureus (MRSA) isolates; we further investigated these as well as the proportion of PVL, encoded by lukS/F-PV, in 761 S. aureus isolates from patients with a diagnosis of pneumonia/lower respiratory tract, skin/soft tissue, bone and joint infection. S. aureus isolates from blood culture were identified and antimicrobial susceptibility testing was performed using automated systems. Conventional PCR assays were used to identify the ccr and mec gene complexes in mecA-positive isolates with an unknown SCCmec type and screen for lukS/F-PV. Epidemiological data was used to classify isolates as healthcare- or community-associated infections. Antimicrobial susceptibility profiles according to SCCmec type and PVL were reported. Of the unknown SCCmec types, isolates were interpreted as type I-like (86%, 38/44), type II-like (9%, 4/44) and type III-like (5%, 2/44). Eight isolates did not produce definitive results. Of all MRSA isolates, majority were multidrug-resistant as indicated by their non-susceptibility to most antimicrobial agents; 92% were healthcare-associated. PVL was seen in 14% of the isolates (MRSA: 25%, MSSA: 75%); 56% were classified as healthcare-associated infection. The SCCmec typing method did not definitively classify all unknown isolates into clearly defined types. It showed that majority of these isolates were not the conventional types; untypeable elements appeared to be composite SCCmec elements, consisting of multiple ccr gene complexes. Majority of the MRSA isolates were non-susceptible to most antibiotics indicating that multiple resistance genes are present in our population. Furthermore, the proportion of PVL was low and more prevalent in MSSA.

We aimed to provide an analysis of A. baumannii complex (ABC) isolated from blood cultures in South Africa. ABC surveillance was conducted from 1 April 2017 to 30 September 2019 at 19 hospital sites from blood cultures of any age and sex. Organism identification was performed using the MALDI-TOF MS and antimicrobial susceptibility testing (AST), MicroScan Walkaway System. We confirmed colistin resistance with Sensititre, FRCOL panel, and selected for whole-genome sequencing. During the study period, we identified 4822 cases of ABC, of which 2152 cases were from 19 enhanced surveillance sites were reported during the enhanced surveillance period (1 August 2018 to 30 September 2019). Males accounted for 54% (2611/4822). Of the cases with known age, 41% (1968/4822) were infants (< 1-year-old). Seventy-eight percent (1688/2152) of cases had a known hospital outcome, of which 36% (602/1688) died. HIV status was known for 69% (1168/1688) of cases, and 14% (238/1688) were positive. Eighty-two percent (1389/1688) received antimicrobial treatment in admission. Three percent (35/1389) of cases received single colistin. Four percent (75/2033) were resistant to colistin. At least 75% of the isolates (1530/2033) can be classified as extensively drug-resistant (XDR), with resistance to most antibiotics except for colistin. The majority, 83% (20/24), of the colistin-resistant isolates were of the sequence type (ST) 1. Resistance genes, both plasmid- and chromosomal- mediated were not observed. Although all isolates had, nine efflux pump genes related to antimicrobial resistance. Our surveillance data contributed to a better understanding of the natural course of A. baumannii disease, the patient characteristics among infants, and the level of resistance. At least two-thirds of the isolates were extensively drug-resistant, and four percent of isolates were resistant to colistin.

The laboratory plays a significant role in public health surveillance, outbreak investigation and infection prevention and control strategies. Microbiology laboratories are moving towards incorporating molecular biology techniques for the surveillance and identification of pathogens causing infectious diseases as well as the genotypic characterisation of these organisms. These methods are accurate, rapid, reliable, and provide a wealth of information that are not available using conventional phenotypic methods. However, establishing such a laboratory can be challenging in developing countries due to poor infrastructure, the lack of funding and the required expertise. This manuscript discusses the essential issues that need to be addressed when establishing a molecular microbiology laboratory and the usefulness of molecular techniques in public health surveillance and outbreaks in developing countries. Molecular data on South African findings obtained from surveillance and outbreak studies are also presented in this manuscript.

(1) Background: The emergence of multidrug resistance enterococci is a major public health concern. This study aimed to determine the prevalence and antimicrobial resistance of enterococci isolated from blood cultures over a five-year period (2016–2020) at public hospitals in South Africa. (2): Methods: A retrospective analysis of clinical enterococci isolated from bloodstream infection samples at the South African public hospitals was conducted. The ESKAPE dataset from January 2016 to December 2020 was obtained from the central data warehouse (CDW) at the National Health Laboratory Service (NHLS). (3): Results: Following de-duplication, a total of 130,352/306,592 organisms isolated from blood cultures were identified as ESKAPE pathogens. In this study, K. pneumoniae (25%; 33,082/130,352), was the most frequently isolated pathogen from blood cultures, followed by S. aureus (23%; 29,922/130,352) and enterococci (16%; 21,339/130,352). Of the enterococci cases, about 43% (9132/21,339) of cases were from the infants aged (<1-year old) and 32% (6745/21,339) from the adult patients. No changes observed in vancomycin, teicoplanin, and linezolid susceptibility; however, E. faecium and E. faecalis blood culture isolates remained highly susceptible (>97%) to these antibiotics. (4): Conclusions: The current study revealed a significant increase of E. faecalis and E. faecium blood culture isolates as compared to the previous national ESKAPE data. Low vancomycin resistance was observed. Continuous monitoring of antimicrobial resistant Enterococcus species is warranted in South Africa.

Background We aimed to describe an outbreak of cutaneous abscesses caused by Panton-Valentine leukocidin (PVL)-producing methicillin-susceptible Staphylococcus aureus (MSSA) among gold mine workers. Methods In February 2018, we retrospectively reviewed a random sample of 50 medical records from 243 cases and conducted face-to-face interviews using a structured questionnaire. Pus aspirates were sent to the National Institute for Communicable Diseases from prospectively-identified cases (November 2017–March 2018). Nasopharyngeal swabs were collected during a colonisation survey in February 2018. Staphylococcus aureus isolates were screened with a conventional PCR for lukS/F -PV. Pulsed-field gel electrophoresis (PFGE) was performed to determine the genetic relatedness among the isolates. A sample of isolates were selected for whole genome sequencing (WGS). We conducted an assessment on biological risks associated with mining activities. Results From January 2017 to February 2018, 10% (350/3582) of mine workers sought care for cutaneous abscesses. Forty-seven medical files were available for review, 96% were male ( n  = 45) with a mean age of 43 years (SD = 7). About 52% (24/46) were involved in stoping and 28% (13/47) worked on a particular level. We cultured S. aureus from 79% (30/38) of cases with a submitted specimen and 14% (12/83) from colonisation swabs. All isolates were susceptible to cloxacillin. Seventy-one percent of S. aureus isolates (30/42) were PVL-PCR-positive. Six PFGE clusters were identified, 57% (21/37) were closely related. WGS analysis found nine different sequence types. PFGE and WGS analysis showed more than one cluster of S. aureus infections involving closely related isolates. Test reports for feed and product water of the mine showed that total plate counts were above the limits of 1000 cfu/ml, coliform counts > 10 cfu/100 ml and presence of faecal coliforms. Best practices were poorly implemented as some mine workers washed protective clothing with untreated water and hung them for drying at the underground surface. Conclusions PVL-producing MSSA caused an outbreak of cutaneous abscesses among underground workers at a gold mining company. To our knowledge, no other outbreaks of PVL-producing S. aureus involving skin and soft tissue infections have been reported in mining facilities in South Africa. We recommend that worker awareness of infection prevention and control practices be strengthened.

A new biopolymer–silica hybrid material consisting of inulin and tetraethoxysilane (TEOS) for use as an adsorbent was successfully synthesized via the sol–gel method in acidic conditions. The hydrolysis and condensation processes were attained in water/ethanol solution. Three molar ratios of inulin:TEOS (1:1, 1:2, and 2:1) were prepared and dried at various temperatures (50, 60, and 70 °C). The optimized molar ratio of 2:1 with a drying temperature of 70 °C was found to obtain the best morphology and characteristics for absorbent properties. Fourier transform infrared spectroscopy (FTIR) analysis showed a strong interaction between inulin and TEOS, which was also observed using energy dispersive X-ray spectroscopy (EDX). Field emission scanning electron microscopy (FESEM) images revealed the presence of nanoparticles on the rough surface of the hybrid sol–gel. X-ray diffractometer (XRD) analysis showed the amorphous state of the silica network where the inulin existed as an anhydrous crystalline phase. Brunauer–Emmet–Teller (BET) analysis confirmed that the composite was mesoporous, with 17.69 m2/g surface area and 34.06 Å pore size. According to thermogravimetric analysis (TGA) results, the hybrid inulin-TEOS adsorbent was thermally stable under a temperature of 200 °C.

Atrioventricular (AV) block in pregnancy is rare, but it is a serious arrhythmia that needs to be carefully managed in pregnancy. However, as of now, there are no clear guidelines or consensus for intrapartum management. Most of the time, an intrapartum AV block is secondary to hypervagatonic sinus node dysfunction and is treated conservatively. Hypervagatonic sinus node dysfunction has a heterogeneous presentation of AV block, and pseudo-Mobitz type II in labor is rarely reported. We report a case of pseudo-Mobitz type II AV block during pregnancy due to labor pain, which is successfully managed conservatively.

Pericentric inversion of chromosome 9 (inv(9)) is one of the most common variants seen in a normal human karyotype that occurs during meiosis. Despite being categorized as a normal variant, some studies using classical cytogenetics have recently shown that inv(9) could be associated with azoospermia, congenital anomalies, growth retardation, and rarely with abnormal karyotype. However, there is no reported association with cyclopia. Interestingly this genetic variant involves twin fetuses. A 36-year-old multiparous lady with dichorionic diamniotic twin pregnancy presented to the fetomaternal unit with fetal growth restriction at 34 weeks of gestation. An ultrasound scan revealed both have microcephaly, fisting hands, holoprosencephaly, and proboscis suspicious of Patau syndrome. Amniocentesis was not issued due to late pregnancy and guarded prognosis. The mother presented with pre-eclampsia at 35 weeks of gestation. The pregnancy managed to prolong up to 36 weeks after which caesarean section was performed due to the leading twin being in a transverse lie. Two baby twin girls were born 3 minutes apart with microcephaly and cyclops appearance. Chromosomal analysis of both twins revealed similar karyotypes of 46, XX, inv(9)(p11,q13). Pericentric inversion of chromosome 9 is regarded as a normal chromosomal variation in the general population, but in twins with cyclops is considered rare. Early referral to a tertiary hospital for twin management is highly required. It may identify fetuses with such abnormalities and counsel the parents with appropriate management.