Tracking Antimicrobial Resistance Determinants in Diarrheal Pathogens: A Cross-Institutional Pilot Study

Infectious diarrhea affects over four billion individuals annually and causes over a million deaths each year. Though not typically prescribed for treatment of uncomplicated diarrheal disease, antimicrobials serve as a critical part of the armamentarium used to treat severe or persistent cases. Due to widespread over- and misuse of antimicrobials, there has been an alarming increase in global resistance, for which a standardized methodology for geographic surveillance would be highly beneficial. To demonstrate that a standardized methodology could be used to provide molecular surveillance of antimicrobial resistance (AMR) genes, we initiated a pilot study to test 130 diarrheal pathogens (Campylobacter spp., Escherichia coli, Salmonella, and Shigella spp.) from the USA, Peru, Egypt, Cambodia, and Kenya for the presence/absence of over 200 AMR determinants. We detected a total of 55 different determinants conferring resistance to ten different categories of antimicrobials: genes detected in ≥ 25 samples included bla_TEM, tet(A), tet(B), mac(A), mac(B), aadA1/A2, strA, strB, sul1, sul2, qacEΔ1, cmr, and dfrA1. The number of determinants per strain ranged from none (several Campylobacter spp. strains) to sixteen, with isolates from Egypt harboring a wider variety and greater number of genes per isolate than other sites. Two samples harbored carbapenemase genes, bla_OXA-48 or bla_NDM. Genes conferring resistance to azithromycin (ere(A), mph(A)/mph(K), erm(B)), a first-line therapeutic for severe diarrhea, were detected in over 10% of all Enterobacteriaceae tested: these included >25% of the Enterobacteriaceae from Egypt and Kenya. Forty-six percent of the Egyptian Enterobacteriaceae harbored genes encoding CTX-M-1 or CTX-M-9 families of extended-spectrum β-lactamases. Overall, the data provide cross-comparable resistome information to establish regional trends in support of international surveillance activities and potentially guide geospatially informed medical care.

High efficacy of artemether-lumefantrine and declining efficacy of artesunate + sulfadoxine-pyrimethamine against Plasmodium falciparum in Sudan (2010-2015): evidence from in vivo and molecular marker studies

Background

The present paper reports on studies that evaluated artesunate + sulfadoxine-pyrimethamine (AS + SP) which is the first-line drug and artemether-lumefantrine (AL) which is a second-line drug against uncomplicated falciparum malaria in Sudan. This evaluation was performed in twenty studies covering six sentinel sites during five successive annual malaria transmission seasons from 2010 to 2015.

Methods

The standard World Health Organization protocol was used for a follow-up period of 28 days. The frequency distribution of molecular markers for antifolate resistance in dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps) genes was studied in pre-treatment samples in four sites in 2011.

Results

In the nine studies of AL conducted at five sites (n = 595), high PCR-corrected cure rates were found, ranging from 96.8 to 100 %. Among the eleven studies of AS + SP (n = 1013), a decline in the PCR-corrected cure rates was observed in Gedaref in Eastern Sudan: 91.0 % in the 2011–12 season and 86.5 % in the 2014–15 season. In the remaining sites, the AS + SP cure rates ranged between 95.6 and 100 %. The rate of clearance of microscopic gametocytaemia after treatment was not significantly different with AL or AS + SP on days 7, 14, 21 and 28 of follow-up. A total of 371 pre-treatment samples were analysed for molecular markers of SP resistance. The temporal changes and geographical differences in the frequency distribution of SP-resistance genotypes showed evidence of regional differentiation and selection of resistant strains.

Conclusion

The findings of this study call for a need to review the Sudan malaria treatment policy. Epidemiological factors could play a major role in the emergence of drug-resistant malaria in eastern Sudan.

Australian New Zealand Clinical Trials Registry

Trial registration numbers 2011–2012: ACTRN12611001253998, 2013–2015: ACTRN12613000945729

High efficacy of two artemisinin-based combinations: artesunate + sulfadoxine-pyrimethamine and artemether-lumefantrine for falciparum malaria in Yemen

BACKGROUND

Artesunate + sulfadoxine-pyrimethamine (AS + SP) has been the first-line treatment and artemether-lumefantrine (AL) the second-line treatment for uncomplicated falciparum malaria in Yemen since 2005. This paper reports the results of studies conducted to monitor therapeutic efficacy of these two drugs in sentinel sites in Yemen.

METHODS

Eight therapeutic efficacy studies were conducted in six sentinel sites during the period 2009-2013 in Yemen. Five studies were for the evaluation of AS + SP (total of 465 patients) and three studies (total of 268 patients) for the evaluation of AL. The studies were done according to standard WHO protocol 2009 with 28-day follow-up.

RESULTS

In the evaluation of AS + SP, the PCR-corrected cure rate was 98 % (95 % CI 92.2-99.5 %) in one site and 100 % in all of the other four sites. In the sites where AL was evaluated, the PCR-corrected cure rate was 100 % in all the sites. All patients were negative for asexual parasitaemia on day 3 in both the AS + SP and the AL groups. There was a higher rate of clearance of gametocytaemia in the AL-treated group when compared with the AS + SP groups from day 7 onwards.

CONCLUSION

AS + SP remains the effective drug for uncomplicated falciparum malaria in Yemen. AL is also highly effective and can be an appropriate alternative to AS + SP for the treatment of falciparum malaria. AL demonstrated a higher efficacy in clearing microscopic gametocytaemia than AS + SP.

TRIAL REGISTRATION

Trial registration number ACTRN12610000696099.

Non-bacterial etiologies of diarrheal diseases in Afghanistan

BACKGROUND

Microbial diarrheal diseases are one of the leading causes of child morbidity and mortality in developing countries. This study aimed to identify the main causes of non-bacterial diarrhea in Afghanistan.

METHODS

A total of 699 stools were collected from children aged under 5 years who presented with diarrhea at Indira Gandhi and Kandahar hospitals. Frozen aliquots were preserved for screening against rotavirus, astrovirus, adenovirus, norovirus, Cryptosporidium and Giardia, when bacterial cultures tested negative. Tests were performed at the hospitals after laboratory staff were trained and provided with enzyme-immunoassays and equipment. Results were confirmed at the U.S. Naval Medical Research Unit No. 3, Cairo, Egypt.

RESULTS

Of the samples tested, 71.9% (503/699) were infected with one or more pathogens. However, the majority (85.8%; 432/503) showed single infections: rotavirus (72.2%; 329/432), Cryptosporidium (14.1%; 61/432), Giardia (5.1%; 22/432), astrovirus (2.3%; 10/432), adenovirus (1.6%; 7/432) and norovirus (0.7%; 3/432). The remaining 14% (71/503) showed mixed infections of the tested pathogens.

CONCLUSIONS

Non-bacterial pathogens were identified that could enable health officials to adopt more effective treatment and control measures for diarrhea in Afghanistan.

Enteric viral infections as potential risk factors for intussusception

Introduction:  We aimed to identify potential risk factors for intussusception (ISS) among children presenting to two pediatric hospitals in Egypt. Methodology: In this case-control study,  enrolled children < 3 years old with ISS (confirmed radiologically and/or surgically) were  matched by age and gender to controls admitted with acute non-abdominal surgical illnesses. Stool samples were collected and tested for various enteric bacteria, rotavirus, enteric adenoviruses (EA, 40 and 41) and astroviruses using commercially available ELISA diagnostic kits. Results: From December 2004 to May 2009, 158 cases and 425 matched controls were enrolled. A history of diarrhoea and cough over the preceding four weeks of interview were more common in cases than controls, respectively. Children with mothers who had secondary education and above were 2.2 times more likely to have ISS than those whose mothers had a lower level of education. In spite of the low detection rate of EA infection (regardless of diarrhoea history) and asymptomatic rotavirus infection, they were detected in higher frequencies in cases than controls; however, infection with astrovirus and bacterial pathogens did not appear to be associated with increased risk of ISS. Conclusions: History of diarrhoea and cough over the four weeks preceding the study and maternal education above secondary level were potential risk factors for ISS. EA and asymptomatic rotavirus infection were detected in higher frequencies among cases than controls; however, association with ISS cannot be confirmed. Additional research is needed to confirm these findings and evaluate the pathogenesis which may link such infections with ISS.

Burden of Aeromonas hydrophila-associated diarrhea among children younger than 2 years in rural Egyptian community

INTRODUCTION

Between 2004 and 2007, a birth cohort of Egyptian children was analysed to evaluate the epidemiology of enteric diseases.

METHODOLOGY

A stool sample was collected from the study children every two weeks as well as whenever they experienced diarrhea. Samples were tested for routine bacterial pathogens as well as enteropathogenic viruses and parasites. A secondary goal of the study was to evaluate the burden of less commonly reported pathogens including Aeromonas hydrophila.

RESULTS

Of the 348 study subjects, 79 had A. hydrophila isolated from their stool at some point during the study.  Thirty-six children had exclusively symptomatic (S) infections while 33 had exclusively asymptomatic (AS) infections. However, 10 children had both S and AS infections. Among symptomatic cases, A. hydrophila was the sole pathogen isolated 36% of the time. An important aspect of A. hydrophila associated diarrhea was the high level of resistance to cephalosporins.

CONCLUSION

Although relatively uncommon, A. hydrophila was found to be associated with diarrhea among children living in Egypt and was frequently multi-drug resistant.

Enteric pathogens associated with childhood diarrhea in Tripoli-Libya

Stool samples from children < 5 years of age with diarrhea (N = 239) were examined for enteric pathogens using a combination of culture, enzyme-immunoassay, and polymerase chain reaction methods. Pathogens were detected in 122 (51%) stool samples; single pathogens were detected in 37.2% and co-pathogens in 13.8% of samples. Norovirus, rotavirus, and diarrheagenic Escherichia coli (DEC) were the most frequently detected pathogens (15.5%, 13.4%, and 11.2%, respectively); Salmonella, adenovirus, and Aeromonas were detected less frequently (7.9%, 7.1%, and 4.2%). The most commonly detected DEC was enteroaggregative E. coli (5.4%). Resistance to ≥ 3 antimicrobials was observed in 60% (18/30) of the bacterial pathogens. Salmonella resistance to ciprofloxacin (63.1%) has become a concern. Enteric viral pathogens were the most significant causative agents of childhood diarrhea in Tripoli. Bacterial pathogens were also important contributors to pediatric diarrhea. The emergence of ciprofloxacin-resistant Salmonella represents a serious health problem that must be addressed by Libyan health authorities.

Validation of the Dri-Dot Latex agglutination and IgM lateral flow assays for the diagnosis of typhoid fever in an Egyptian population

Laboratory confirmation of typhoid fever is essential for appropriate medical treatment. Blood culture is a standard test for diagnosis of typhoid fever, but well-equipped diagnostic facilities to perform culture are seldom available in endemic areas. We retrospectively compared 2 diagnostic field tests, a latex agglutination Dri-Dot assay and an IgM Lateral Flow assay, to blood culture, in patients with clinically diagnosed typhoid fever. Sensitivity of the Dri-Dot was 71.4%, and specificity was 86.3% for samples collected at time of first diagnosis. Sensitivity and specificity of IgM Lateral Flow were 80% and 71.4%, respectively. A major limitation of these serologic tests is the limited sensitivity at the early stage of the disease. Performing both tests in parallel increased sensitivity to 84.3%, but decreased specificity to 70.5%. There was a trend towards improved diagnostic performance using either assay over a longer duration of illness. These rapid, point-of-care assays for typhoid fever provide easy-to-interpret results in typhoid-endemic countries and may be most useful in patients presenting 1 week after symptom onset.