Outbreak of Listeriosis in South Africa Associated with Processed Meat.

BACKGROUND: An outbreak of listeriosis was identified in South Africa in 2017. The source was unknown. METHODS: We conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type Listeria monocytogenes isolates. A case was defined as laboratory-confirmed L. monocytogenes infection during the period from June 11, 2017, to April 7, 2018. RESULTS: A total of 937 cases were identified, of which 465 (50%) were associated with pregnancy; 406 of the pregnancy-associated cases (87%) occurred in neonates. Of the 937 cases, 229 (24%) occurred in patients 15 to 49 years of age (excluding those who were pregnant). Among the patients in whom human immunodeficiency virus (HIV) status was known, 38% of those with pregnancy-associated cases (77 of 204) and 46% of the remaining patients (97 of 211) were infected with HIV. Among 728 patients with a known outcome, 193 (27%) died. Clinical isolates from 609 patients were sequenced, and 567 (93%) were identified as sequence type 6 (ST6). In a case-control analysis, patients with ST6 infections were more likely to have eaten polony (a ready-to-eat processed meat) than those with non-ST6 infections (odds ratio, 8.55; 95% confidence interval, 1.66 to 43.35). Polony and environmental samples also yielded ST6 isolates, which, together with the isolates from the patients, belonged to the same core-genome multilocus sequence typing cluster with no more than 4 allelic differences; these findings showed that polony produced at a single facility was the outbreak source. A recall of ready-to-eat processed meat products from this facility was associated with a rapid decline in the incidence of L. monocytogenes ST6 infections. CONCLUSIONS: This investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons. Whole-genome sequencing facilitated the detection of the outbreak and guided the trace-back investigations that led to the identification of the source.

Molecular characterisation of clinical and environmental isolates of Mycobacterium kansasii isolates from South African gold mines.

Mycobacterium kansasii (M. kansasii) is a major cause of non-tuberculous mycobacterial pulmonary disease in the South African gold-mining workforce, but the source of infection and molecular epidemiology are unknown. This study investigated the presence of M. kansasii in gold and coal mine and associated hostel water supplies and compared the genetic diversity of clinical and environmental isolates of M. kansasii. Five M. kansasii and ten other potentially pathogenic mycobacteria were cultured mainly from showerhead biofilms. Polymerase chain reaction-restriction analysis of the hsp65 gene on 196 clinical and environmental M. kansasii isolates revealed 160 subtype I, eight subtype II and six subtype IV strains. Twenty-two isolates did not show the typical M. kansasii restriction patterns, suggesting that these isolates may represent new subtypes of M. kansasii. In contrast to the clonal population structure found amongst the subtype I isolates from studies in other countries, DNA fingerprinting of 114 clinical and three environmental subtype I isolates demonstrated genetic diversity amongst the isolates. This study demonstrated that showerheads are possible sources of M. kansasii and other pathogenic non-tuberculous mycobacterial infection in a gold-mining region, that subtype I is the major clinical isolate of M. kansasii strain and that this subtype exhibits genetic diversity.

Epidemic spread of multidrug-resistant tuberculosis in Johannesburg, South Africa.

Numerous reports have documented isolated transmission events or clonal outbreaks of multidrug-resistant Mycobacterium tuberculosis strains, but knowledge of their epidemic spread remains limited. In this study, we evaluated drug resistance, strain diversity, and clustering rates in patients diagnosed with multidrug-resistant (MDR) tuberculosis (TB) at the National Health Laboratory Service (NHLS) Central TB Laboratory in Johannesburg, South Africa, between March 2004 and December 2007. Phenotypic drug susceptibility testing was done using the indirect proportion method, while each isolate was genotyped using a combination of spoligotyping and 12-MIRU typing (12-locus multiple interspersed repetitive unit typing). Isolates from 434 MDR-TB patients were evaluated, of which 238 (54.8%) were resistant to four first-line drugs (isoniazid, rifampin, ethambutol, and streptomycin). Spoligotyping identified 56 different strains and 28 clusters of variable size (2 to 71 cases per cluster) with a clustering rate of 87.1%. Ten clusters included 337 (77.6%) of all cases, with strains of the Beijing genotype being most prevalent (16.4%). Combined analysis of spoligotyping and 12-MIRU typing increased the discriminatory power (Hunter Gaston discriminatory index [HGDI] = 0.962) and reduced the clustering rate to 66.8%. Resolution of Beijing genotype strains was further enhanced with the 24-MIRU-VNTR (variable-number tandem repeat) typing method by identifying 15 subclusters and 19 unique strains from twelve 12-MIRU clusters. High levels of clustering among a variety of strains suggest a true epidemic spread of MDR-TB in the study setting, emphasizing the urgency of early diagnosis and effective treatment to reduce transmission within this community.

Analysis of the Trends of Methicillin-Resistant Staphylococcus aureus in Gauteng Public Hospitals from 2009 to 2018.

Most investigations into the distribution of methicillin resistant Staphylococcus aureus (MRSA) have focused exclusively on bloodborne infections within individual health care institutions for shorter time periods. This has limited the analysis of a community-spread pathogen to snapshots within the hospital domain. Therefore, in this study we determined the demographic and geographical patterns of MRSA infections and their fluctuation in 10 years within all public hospitals in Gauteng, South Africa. A retrospective analysis of S. aureus samples was done by deduplicating samples in two groups. The sample groups were placed into subsets with respect to demographic and geographical fields and compared across the studied period. Logistic regression was utilized to determine odds ratios for resistant infections in univariate and multivariable configurations. A total of 66,071 unique infectious events were identified from the 148,065 samples received over a 10-year period, out of which 14,356 were identified as bacteremia. MRSA bacteremia rates in Gauteng peaked in 2015 and have since decreased. Within Gauteng, metropolitan areas have the greatest burden of MRSA with children under 5 years of age and males being most affected. Medical wards have the highest S. aureus bacteremia rates, while intensive care units have the highest MRSA bacteremia rates. Patient age, admitting ward, and geographical district are the most important associated factors of resistance. MRSA acquisition rates have shown tremendous growth since 2009 but have since spiked and subsequently decreased. This may be due to the initiation of the National Guidelines on Antimicrobial Stewardship and Infectious Disease Surveillance. Further studies to determine the trajectory of infections are required to support these claims. IMPORTANCE S. aureus is the leading cause of a variety of devastating clinical conditions, including infective endocarditis, bacteremia, and pleuropulmonary infections. It is an important pathogen responsible for substantial morbidity and mortality. MRSA is a variant of interest originally responsible for difficult to treat hospital-acquired infections that has since achieved community spread throughout the world. Most investigations into the distribution of MRSA have focused exclusively on bloodborne infections within individual health care institutions for shorter periods. This has limited the analysis of a community-spread pathogen to snapshots within the hospital domain. This study sought to determine the demographic and geographical patterns of MRSA infections as well as how these have fluctuated over time within all public hospitals. This will also help in understanding the epidemiology and resistance trends of S. aureus, which will help clinicians to understand the clinical prospective and policy makers to design guidelines and strategies for treating such infections.

The nucleoside reverse transcriptase inhibitors didanosine, lamivudine, stavudine and zidovudine show little effect on the virulence of Candida albicans in vitro.

Nucleoside reverse transcriptase inhibitors (NRTIs) are used in the treatment of human immunodeficiency virus (HIV). Since the analogue 5-fluorouracil increases Candida albicans virulence in vitro, and zidovudine therapy is associated with enhanced C. albicans adherence and biofilm formation, we investigated the effects of commonly used NRTIs on the virulence of C. albicans isolated from 21 antiretroviral-naïve HIV/AIDS patients. The isolates were exposed to didanosine, lamivudine, stavudine and zidovudine at their expected patient serum peak levels and at one-half and two times these levels for 24h and 72 h. Assays assessing changes in adherence, proliferation, biofilm formation and antifungal susceptibility were performed. No differences in these virulence characteristics of isolates exposed to NRTIs were noted in most cases. However, at 24h and 72 h a significant increase in the rate of proliferation was observed in response to two-fold the peak concentration of lamivudine. The results suggest a limited effect of NRTIs on C. albicans virulence.

Synergistic antifungal effect of cyclized chalcone derivatives and fluconazole against Candida albicans.

The occurrence of invasive fungal diseases, particularly in immunocompromised patients, is life-threatening and increases the economic burden. The rising problem of multi-drug resistance is becoming a major concern for clinicians. In addition, a repertoire of antifungal agents is far less in number than antibacterial drugs. To combat these problems, combination therapy has gained a lot of interest. We previously reported the synergistic interaction of some mono- and bis-dihydropyrimidinone and thione derivatives with fluconazole and amphotericin B for combination antifungal therapy. In this study we used the same approach and synthesized different azole and non-azole derivatives of mono-(M) and bis-(B) chalcones and evaluated their antifungal activity profile alone and in combination with the most commonly used antifungal drug - fluconazole (FLC) - against seven FLC susceptible and three FLC resistant clinically isolated Candida albicans strains. Based on the minimum inhibitory concentration results, the bis-derivatives showed lower MIC values compared to their mono-analogues. Both fractional inhibitory concentration index and isobologram results revealed mostly synergistic, additive or indifferent interactions between the tested compounds and FLC against different Candida isolates. None of the tested compounds showed any effect on energy dependent R6G efflux, revealing that they do not reverse the mechanism of drug efflux. However, surprisingly, these compounds profoundly decreased ergosterol biosynthesis and showed down regulation of ERG11 gene expression, which is the possible mechanism of reversal of azole drug resistance by these compounds. These results provide a platform for further research to develop pyrimidinone/thione ring containing compounds as promising new antifungal agents, which could be used in antifungal combination therapy.

Automated image processing method for the diagnosis and classification of malaria on thin blood smears.

Malaria is a serious global health problem, and rapid, accurate diagnosis is required to control the disease. An image processing algorithm to automate the diagnosis of malaria on thin blood smears is developed. The image classification system is designed to positively identify malaria parasites present in thin blood smears, and differentiate the species of malaria. Images are acquired using a charge-coupled device camera connected to a light microscope. Morphological and novel threshold selection techniques are used to identify erythrocytes (red blood cells) and possible parasites present on microscopic slides. Image features based on colour, texture and the geometry of the cells and parasites are generated, as well as features that make use of a priori knowledge of the classification problem and mimic features used by human technicians. A two-stage tree classifier using backpropogation feedforward neural networks distinguishes between true and false positives, and then diagnoses the species (Plasmodium falciparum, P. vivax, P. ovale or P. malariae) of the infection. Malaria samples obtained from the Department of Clinical Microbiology and Infectious Diseases at the University of the Witwatersrand Medical School are used for training and testing of the system. Infected erythrocytes are positively identified with a sensitivity of 85% and a positive predictive value (PPV) of 81%, which makes the method highly sensitive at diagnosing a complete sample provided many views are analysed. Species were correctly determined for 11 out of 15 samples.

Antimicrobial resistance in developing countries. Part I: recent trends and current status.

The global problem of antimicrobial resistance is particularly pressing in developing countries, where the infectious disease burden is high and cost constraints prevent the widespread application of newer, more expensive agents. Gastrointestinal, respiratory, sexually transmitted, and nosocomial infections are leading causes of disease and death in the developing world, and management of all these conditions has been critically compromised by the appearance and rapid spread of resistance. In this first part of the review, we have summarised the present state of resistance in these infections from the available data. Even though surveillance of resistance in many developing countries is suboptimal, the general picture is one of accelerating rates of resistance spurred by antimicrobial misuse and shortfalls in infection control and public health. Reservoirs for resistance may be present in healthy human and animal populations. Considerable economic and health burdens emanate from bacterial resistance, and research is needed to accurately quantify the problem and propose and evaluate practicable solutions. In part II, to be published next month, we will review potential containment strategies that could address this burgeoning problem.

Antimicrobial resistance in developing countries. Part II: strategies for containment.

The growing threat from resistant organisms calls for concerted action to prevent the emergence of new resistant strains and the spread of existing ones. Developing countries have experienced unfavourable trends in resistance-as detailed in part I, published last month--and implementation of many of the containment strategies recommended by WHO is complicated by universal, as well as developing country-specific, factors. The control of selective pressure for resistance could potentially be addressed through educational and other interventions for orthodox and unorthodox prescribers, distributors, and consumers of antimicrobials. At national levels, the implementation of drug use strategies--eg, combination therapy or cycling--may prove useful to lengthen the lifespan of existing and future agents. Programmes such as the Integrated Management of Childhood Illnesses (IMCI) and directly observed short-course therapy (DOTS) for tuberculosis are prescriber-focused and patient-focused, respectively, and have both been shown to positively influence factors that contribute to the selective pressure that affects resistance. The institution of interventions to prevent the transmission of infectious diseases could also lead to beneficial effects on the prevalence of resistance, as has vaccination against Haemophilus influenzae type B and Streptococcus pneumoniae. There has been an upsurge in the number of organisations and programmes that directly address issues of resistance, and collaboration could be one way to stem the dire trend. Additional factors such as unregulated drug availability, inadequate antimicrobial drug quality assurance, inadequate surveillance, and cultures of antimicrobial abuse must be addressed to permit a holistic strategy for resistance control.

Interhospital transfer of pan-resistant Acinetobacter strains in Johannesburg, South Africa.

BACKGROUND: Acinetobacter species infections are increasingly found to cause nosocomial infections, particularly in intensive care units. These pathogens are difficult to eliminate from the hospital environment, and the emergence of multiple-drug-resistant strains complicates patient treatment. In this retrospective study, several strains were analyzed to study the possible spread of pan-resistant strains. METHODS: Macrorestriction analysis was performed on isolates collected in July 2001 from Johannesburg Hospital and strains collected from a number of hospitals in Johannesburg a year later. RESULTS: A strain endemic to Johannesburg Hospital that was cefepime and ceftazidime sensitive in 2001 developed resistance to these antibiotics within 1 year. This and other resistant strains were found to have spread among academic and private hospitals in the area by July 2002. CONCLUSIONS: The development of resistance is believed to be a response to antibiotic pressure and the spread of resistant strains a result of health care worker and/or patient transfer among hospitals. This snapshot epidemiologic study highlights the need to institute stricter infection control measures to limit the spread of organisms such as Acinetobacter among hospitals.