Bacterial bloodstream infections in HIV-infected adults attending a Lagos teaching hospital

[Antibacterial Susceptibility Patterns of Bloodstream Isolates in 74 HIV-Infected Patients Hospitalized at the Clinic of Infectious and Tropical Diseases of Fann University Hospital, Dakar from 2013 to 2016]

Introduction

Bacteremia is associated with high lethality in HIV-infected patients. The widespread use of cotrimoxazole prophylaxis and misuse of antibiotics promote antibacterial resistance. Only few studies have considered this issue in HIV-infected patients. Thus, the objective of this study was to describe the etiology and antibacterial susceptibility patterns of bloodstream isolates in patient living with HIV.

Material and methods

This is a retrospective cross-sectional and descriptive study conducted at the clinic of Infectious and Tropical Diseases of Fann university hospital from March 2013 to December 2016. Data were collected from patients' files according to a pre-establish survey form made of demographic, clinical, bacteriological and biological parameters.

Results

Seventy-four cases of bacteremia were registered, 51.4% of which in women. Participants' median age was 45 years old [18-73 years old] and average CD4 count 83.3 cells/μl. The most commonly isolated bacteria were coagulase negative staphylococci (14%) followed by Escherichia coli (10%) and Klebsiella pneumoniae (10%). Rates of methicillin resistance for coagulase negative staphylococci and Staphylococcus aureus were 35.7% (5/14) and 22% (2/9), respectively. The most frequent ESBL producing germs were Escherichia coli 50% (5/10), Klebsiella pneumoniae 40% (4/10) and Enterobacter sp 25% (2/8). Pseudomonas sp were the most (22.2%) germs resistant to carbapenems.

Conclusion

The result of this study advocates the need for ongoing surveillance of antibacterial resistance in HIV-infected patients and empirical antibiotic therapy based on surveillance data.

Multidrug-Resistant Coagulase-Negative Staphylococci Isolated from Bloodstream in the uMgungundlovu District of KwaZulu-Natal Province in South Africa: Emerging Pathogens

Coagulase-negative staphylococci (CoNS) are increasingly associated with nosocomial infections, especially among the immunocompromised and those with invasive medical devices, posing a significant concern. We report on clinical multidrug-resistant CoNS from the uMgungundlovu District, KwaZulu-Natal Province, South Africa, as emerging pathogens. One hundred and thirty presumptive CoNS were obtained from blood cultures. Culture, biochemical tests, and the Staphaurex™ Latex Agglutination Test were used for the initial identification of CoNS isolates; confirmation and speciation were undertaken by the VITEK 2 system. Susceptibilities of isolates against a panel of 20 antibiotics were determined using the Kirby-Bauer disk diffusion method, and the multiple antibiotic resistance (MAR) indices of the isolates were determined. The polymerase chain reaction (PCR) was used to amplify the mecA gene to confirm methicillin resistance. Overall, 89/130 presumptive CoNS isolates were confirmed as CoNS by the VITEK 2 system. Of these, 68 (76.4%) isolates were putatively methicillin-resistant by the phenotypic cefoxitin screen test and 63 (92.6%) were mecA positive. Staphylococcus epidermidis (19.1%), S. hominis ssp. hominis (15.7%), and S. haemolyticus (16.9%) were the most common CoNS species. Isolates showed high percentage resistance against penicillin (100.0%), erythromycin (74.2%), and azithromycin (74.2%) while displaying high susceptibilities to linezolid (95.5%), gentamicin (95.5%), and tigecycline (94.4%). Multidrug resistance (MDR) was observed in 76.4% of isolates. MAR index calculation revealed 71.9% of isolates with MAR index >0.2 and 20.2% >0.5. Isolates with the highest MAR indices (0.7 and 0.8) were recovered from the neonatal intensive care unit. Fifty-one MDR antibiograms were observed. The high prevalence of methicillin resistance and multidrug resistance in several species of CoNS necessitates surveillance of this emerging pathogen, currently considered a contaminant of microbial cultures.

Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans, whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences-including a novel SC isolate-revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large-scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

The Genus Ochrobactrum as Major Opportunistic Pathogens

Ochrobactrum species are non-enteric, Gram-negative organisms that are closely related to the genus Brucella. Since the designation of the genus in 1988, several distinct species have now been characterised and implicated as opportunistic pathogens in multiple outbreaks. Here, we examine the genus, its members, diagnostic tools used for identification, data from recent Ochrobactrum whole genome sequencing and the pathogenicity associated with reported Ochrobactrum infections. This review identified 128 instances of Ochrobactrum spp. infections that have been discussed in the literature. These findings indicate that infection review programs should consider investigation of possible Ochrobactrum spp. outbreaks if these bacteria are clinically isolated in more than one patient and that Ochrobactrum spp. are more important pathogens than previously thought.

Emerging and re-emerging bacterial zoonoses in Nigeria: current preventive measures and future approaches to intervention

A characteristic of bacterial zoonoses, diseases caused by bacteria that can be transmitted to humans from animals, is a propensity to re-emerge. Several studies demonstrate their ongoing transmission in Nigeria, the most populous country in Africa. However, as local epidemiological data on bacterial zoonoses are inadequate the extent and impact of these infectious diseases is under-reported. Consequently, they are not a targeted priority of national public health policies. This limited recognition is despite indications of their possible roles in the widespread prevalence of non-malarial undifferentiated fever in Nigeria. While a number of animal reservoirs and arthropod vectors have been identified in the transmission routes of these diseases, an escalation of cases of undiagnosed febrile illness highlights the urgent need for a comprehensive assessment of other potential reservoirs, vectors and transmission cycles that may increase the local risk of infection with bacterial zoonoses. Animal health interventions have been proposed as a cost-effective strategy. Here, we present a broad overview of bacterial zoonotic infections of humans in Nigeria in the context of evolving epidemiological patterns. Further, we propose that facilitating the operation of a community-based One Health program is essential to providing the comprehensive epidemiological information that is required to improve prioritization of bacterial zoonoses. This would provide a driver for much needed investment in relevant public health interventions in Africa's most populous country.

Review of Clinically and Epidemiologically Relevant Coagulase-Negative Staphylococci in Africa

Coagulase-negative staphylococci (CoNS) have engendered substantial interest in recent years as pathogenic causes of infections in both human and veterinary medicine, especially in the immunocompromised, critically ill, long-term hospitalized and in those harboring invasive medical devices such as catheters. They have been implicated in infections such as urinary tract infections, bloodstream infections, and invasive device-related infections, and are responsible for substantial economic losses in livestock production. The advancement of diagnostic techniques has increased our understanding of their molecular mechanisms of pathogenicity, even though distinguishing between innocuousness and pathogenicity is still challenging. The incidence of CoNS varied across the continent in humans and animals (mainly cattle), ranging from 6% to 68% in suspected human infections and from 3% to 61.7% in suspected animal infections, distributed across different geographic locations. Furthermore, there were varying antibiotic resistance patterns observed in CoNS isolates, with high methicillin resistance in some cases, leading to crossresistance against many antibiotics. Staphylococcus epidermidis, Staphylococcus haemolyticus, and Staphylococcus xylosus were most commonly reported in studies herein reviewed, while the enterotoxin C gene, atl E gene, ica gene, and hemolysin virulence factors were linked with enhanced pathogenicity. Advancement in identification and typing methods, including whole genome sequencing, virulence screening, and the assessment of the immune status of subjects in studies will help to thoroughly assess the true pathogenic potential of isolated CoNS species in developing countries. Careful antibiotic stewardship guidelines should be followed due to the ability of CoNS to develop multidrug resistance.

Current diagnostic methods for HIV

Detection of HIV infection is essential for diagnosis and monitoring of the infection. There are different types of diagnostic tools available that are based on detection of HIV-specific antibodies, viral antigen or nucleic acid. Sensitivities and specificities of assays utilized for HIV detection have improved. Newer HIV testing technologies such as third-generation enzyme immunoassay which detect HIV-specific IgG and IgM antibodies, fourth-generation enzyme immunoassay which detect both anti-HIV antibodies and HIV p24 antigen and nucleic acid based tests for HIV RNA have significantly decreased the window period. This review provides an overview of current technologies for the detection and monitoring of HIV infection and recent advances in the field of HIV diagnosis.

A Systematic Review of the Incidence, Risk Factors and Case Fatality Rates of Invasive Nontyphoidal Salmonella (iNTS) Disease in Africa (1966 to 2014)

This study systematically reviews the literature on the occurrence, incidence and case fatality rate (CFR) of invasive nontyphoidal Salmonella (iNTS) disease in Africa from 1966 to 2014. Data on the burden of iNTS disease in Africa are sparse and generally have not been aggregated, making it difficult to describe the epidemiology that is needed to inform the development and implementation of effective prevention and control policies. This study involved a comprehensive search of PubMed and Embase databases. It documents the geographical spread of iNTS disease over time in Africa, and describes its reported incidence, risk factors and CFR. We found that Nontyphoidal Salmonella (NTS) have been reported as a cause of bacteraemia in 33 out of 54 African countries, spanning the five geographical regions of Africa, and especially in sub-Saharan Africa since 1966. Our review indicates that NTS have been responsible for up to 39% of community acquired blood stream infections in sub-Saharan Africa with an average CFR of 19%. Salmonella Typhimurium and Enteritidis are the major serovars implicated and together have been responsible for 91%% of the cases of iNTS disease, (where serotype was determined), reported in Africa. The study confirms that iNTS disease is more prevalent amongst Human Immunodeficiency Virus (HIV)-infected individuals, infants, and young children with malaria, anaemia and malnutrition. In conclusion, iNTS disease is a substantial cause of community-acquired bacteraemia in Africa. Given the high morbidity and mortality of iNTS disease in Africa, it is important to develop effective prevention and control strategies including vaccination.

Etiologic Agents of Bacterial Sepsis and Their Antibiotic Susceptibility Patterns among Patients Living with Human Immunodeficiency Virus at Gondar University Teaching Hospital, Northwest Ethiopia

Background. Bacterial sepsis is a major cause of illness in human immunodeficiency virus infected patients. There is scarce evidence about sepsis among HIV patients in Ethiopia. This study aimed to determine the etiologic agents of bacterial sepsis and their antibiotic susceptibility patterns among HIV infected patients. Methods. A cross-sectional study was carried out from March 1 to May 2, 2013. One hundred patients infected with HIV and suspected of having sepsis were included. Sociodemographic data were collected by interview and blood sample was aseptically collected from study participants. All blood cultures were incubated aerobically at 35°C and inspected daily for 7 days. The positive blood cultures were identified following the standard procedures and antimicrobial susceptibility testing was performed using disk diffusion technique. Data was entered by Epi-info version 3.5.1 and analysis was done using SPSS version 20. Results. Of the study participants, 31 (31%) confirmed bacterial sepsis. The major isolates were 13 (13%) Staphylococcus aureus, 8 (8%) coagulates negative staphylococci, and 3 (3%) viridans streptococci. Majority of the isolates, 25 (80.6%), were multidrug resistant to two or more antimicrobial agents. Conclusions. Bacterial sepsis was a major cause of admission for HIV infected patients predominated by Staphylococcus aureus and coagulase negative staphylococci species and most of the isolates were multidrug resistant.

Microbiology, genomics, and clinical significance of the Pseudomonas fluorescens species complex, an unappreciated colonizer of humans

Pseudomonas fluorescens is not generally considered a bacterial pathogen in humans; however, multiple culture-based and culture-independent studies have identified it at low levels in the indigenous microbiota of various body sites. With recent advances in comparative genomics, many isolates originally identified as the "species" P. fluorescens are now being reclassified as novel Pseudomonas species within the P. fluorescens "species complex." Although most widely studied for its role in the soil and the rhizosphere, P. fluorescens possesses a number of functional traits that provide it with the capability to grow and thrive in mammalian hosts. While significantly less virulent than P. aeruginosa, P. fluorescens can cause bacteremia in humans, with most reported cases being attributable either to transfusion of contaminated blood products or to use of contaminated equipment associated with intravenous infusions. Although not suspected of being an etiologic agent of pulmonary disease, there are a number of reports identifying it in respiratory samples. There is also an intriguing association between P. fluorescens and human disease, in that approximately 50% of Crohn's disease patients develop serum antibodies to P. fluorescens. Altogether, these reports are beginning to highlight a far more common, intriguing, and potentially complex association between humans and P. fluorescens during health and disease.

Prevalência de bactérias gram-negativas em portadores de HIV internados em serviço especializado

Resumo Objetivo: Identificar a prevalência de bactérias gram-negativas em portadores de HIV internados em serviço especializado. Métodos: Trata-se de um estudo de corte transversal, foram abordados 365 indivíduos internados em duas unidades especializadas, de um hospital escola do interior paulista, sendo a população composta por 220 sujeitos. Os dados sociodemográficos e clínicos e foram obtidos por meio de entrevista individual e consulta aos prontuários. Coletaram-se também amostras de saliva e secreção nasal nas primeiras 24 horas de internação. Resultados: A prevalência de bactérias gram-negativas em portadores de HIV foi de 14,5 % independente do sítio onde foi isolado. Pseudomonas aeruginosa foi o microorganismo mais frequentemente isolado, seguida por Klebsiella pneumoniae. Conclusão: A identificação de bactérias gram-negativas foi maior na saliva (11,8%) que na secreção nasal (3,6%), indicando que coletar amostras de mais de um sítio pode favorecer a identificação de indivíduos colonizados e ou infectados.

Antimicrobial susceptibility patterns of enterobacteriaceae isolated from HIV-infected patients in Kinshasa

Introduction

People infected by Human Immunodeficiency Virus (HIV) are susceptible to develop severe bacterial infections. We set out to determine the frequency and the sensitivity to antibiotics of enterobaceriaceae isolated from urine and feces of HIV-infected persons.

Methods

Urine and feces samples were collected from HIV-infected patients of the Centre de Traitement Ambulatoire de Kabinda (CTA/Kabinda, Kinshasa) and analyzed at the Reference National Laboratory for HIV/AIDS and Sexually Transmitted Infections. The isolated enterobacteriaceae strains were identified by conventional microbiological methods. Antibiotic sensitivity pattern was carried out by disc diffusion method.

Results

The following bacteria pathogens were isolated: Escherichia coli, Klebsiella, Enterobacter, Proteus, and Providencia. Most species were sensitive to cefotaxim, ceftriaxon, and gentamicin and resistant to chloramphenicol, cotrimoxazole, tetracycline, and norfloxacin.

Conclusion

The results of the present study show that the most frequently bacteria isolated were Esherichia coli and cefotaxim, ceftriaxon, and gentamicin were the most active antibiotics.

Antimicrobial resistance determinants in Staphylococcus spp. recovered from birds of prey in Portugal

Antibiotic resistance among wild animals represent an emerging public health concern. The objective of this study was to analyze the staphylococcal nasal microbiota in birds of prey and their content in antimicrobial resistance determinants. Nasal samples from 16 birds of prey were collected, swabs were dipped and incubated into BHI broth [6.5% NaCl] and later seeded on manitol salt agar and oxacillin-resistance screening agar base media. Staphylococcal colonies were isolated from both media and were identified by biochemical and molecular methods. Susceptibility testing to 18 antimicrobial agents was performed by disk-diffusion method. Six of the 16 tested animals carried staphylococci (37.5%) and 7 isolates of the following species were recovered: Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus saprophyticus, Staphylococcus sciuri rodentium, Staphylococcus cohnii urealitycum, and Staphylococcus gallinarum. The S. aureus isolate was penicillin-resistant (with blaZ gene) but methicillin-susceptible and was ascribed to spa-type t012, sequence-type ST30 and agr-type III. The S. epidermidis isolate carried blaZ, mecA, mrs(A/B), mphC, tet(K), drfA, and fusC genes, ica operon, and was typed as ST35. The genes ant6'-Ia, tet(K), tet(L), dfrG, cat221, cat194, and cat223 were detected in S. saprophyticus or S. gallinarum isolates. Birds of prey seem to be a natural reservoir of S. aureus and coagulase-negative staphylococci resistant to multiple antibiotics. Due to the convergence between habitats, the contact between wildlife, other animals and humans is now more common and this involves an increased possibility of interchange of these microorganisms in the different ecosystems.

Bacteremia as a cause of fever in ambulatory, HIV-infected Mozambican adults: results and policy implications from a prospective observational study

Fever is typically treated empirically in rural Mozambique. We examined the distribution and antimicrobial susceptibility patterns of bacterial pathogens isolated from blood-culture specimens, and clinical characteristics of ambulatory HIV-infected febrile patients with and without bacteremia. This analysis was nested within a larger prospective observational study to evaluate the performance of new Mozambican guidelines for fever and anemia in HIV-infected adults (clinical trial registration NCT01681914, www.clinicaltrials.gov); the guidelines were designed to be used by non-physician clinicians who attended ambulatory HIV-infected patients in very resource-constrained peripheral health units. In 2012 (April-September), we recruited 258 HIV-infected adults with documented fever or history of recent fever in three sites within Zambézia Province, Mozambique. Although febrile patients were routinely tested for malaria, blood culture capacity was unavailable in Zambézia prior to study initiation. We confirmed bacteremia in 39 (15.1%) of 258 patients. The predominant organisms were non-typhoid Salmonella, nearly all resistant to multiple first-line antibiotics (ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole). Features most associated with bacteremia included higher temperature, lower CD4+ T-lymphocyte count, lower hemoglobin, and headache. Introduction of blood cultures allowed us to: 1) confirm bacteremia in a substantial proportion of patients; 2) tailor specific antimicrobial therapy for confirmed bacteremia based on known susceptibilities; 3) make informed choices of presumptive antibiotics for patients with suspected bacteremia; and 4) construct a preliminary clinical profile to help clinicians determine who would most likely benefit from presumptive bacteremia treatment. Our findings demonstrate that in resource-limited settings, there is urgent need to expand local microbiologic capacity to better identify and treat cases of bacteremia in HIV-infected and other patients, and to support surveillance. Data on the prevalence and susceptibility patterns of important pathogens can guide national formulary and prescribing practices.

Coagulase-negative staphylococci in an HIV-infected child causing pancytopaenia

Although coagulase-negative staphylococci (CONS) constitute normal flora of the human body, some species can produce human infections, particularly when the host defense is breached. There is little evidence of the pathogenicity of CONS in HIV-infected individuals. We present the case of a 14-year-old HIV-infected boy who presented with a right lower zone pneumonia and a cutaneous abscess, following which he developed pancytopaenia due to underlying CONS infection that responded to antibiotic treatment.

Erythema nodosum associated with Staphylococcus xylosus septicemia

Staphylococcus xylosus is a coagulase-negative staphylococcus. It is a commensal bacterium associated with skin and mucous membranes and occasionally it can cause human infections. We report the first case of erythema nodosum developed in a young woman with S. xylosus septicemia and specific serum antibody response.

Bacteriologic and plasmid analysis of etiologic agents of conjunctivitis in Lagos, Nigeria

BACKGROUND

Conjunctivitis, an inflammation of the conjunctiva, is one of the most common eye problems affecting all age groups in Nigeria. A better understanding of its epidemiology and the antibiotic susceptibility of etiologic bacterial agents is crucial for the initiation of preventive and therapeutic measures. This study determined the distribution and patterns of bacterial infections in Nigerian patients with conjunctivitis. Antibiotic resistance patterns and the plasmid profiles of these pathogens were also investigated.

METHODOLOGY

A total of 83 consecutive and non-duplicate conjunctival specimens were collected from patients attending eye clinics at three different hospitals in Lagos, Nigeria, between February and September 2010. Specimens were cultured on standard bacteriologic media and the recovered isolates speciated using standard techniques. Susceptibility of pathogens to antibiotics and plasmid DNA extraction were carried out by disk diffusion and alkaline lysis methods. Conjugation experiment was done with rifampicin-resistant Escherichia coli DH5α as the recipient cell. Data were analyzed using the chi-square test.

RESULTS

All the specimens were culture-positive, yielding a total of 155 bacterial isolates. Gram-positive cocci comprising Staphylococcus aureus (27.7%) and coagulase-negative Staphylococcus sp. (22.6%) accounted for 50.3% (78 of 155) of conjunctivitis cases, followed by Gram-positive bacilli (22.6%), Gram-negative bacilli (21.3%), and Gram-negative cocci (4.5%). Corynebacterium spp. were the most commonly isolated Gram-positive bacilli accounting for 16.1% of conjunctivitis cases. Pseudomonas aeruginosa topped with 9.7% as the most commonly isolated Gram-negative bacilli. Other Gram-negative bacilli in order of their isolations were E. coli (6.5%), Proteus sp. (3.2%), Klebsiella sp. (1.9%), and Enterobacter aerogenes (1.9%). Moraxella spp. were the only Gram-negative cocci isolated, and they accounted for 4.5% of the total conjunctival infections. Further analysis of the complexity of infections showed that 25 specimens elicited mono-infections, while cases of polymicrobial infections caused by two pathogens and three or more pathogens constituted 51.8% and 18.1% of conjunctivitis specimens screened, respectively. The disparity in the percentage contribution of three infection patterns was significant (P < 0.05). Antibiotic susceptibility testing revealed chloramphenicol and ofloxacin as the least and most active antibiotics tested as 99 (63.9%) and 149 (96.1%) of the 155 recovered isolates were sensitive to them. On the whole, the least susceptible pathogen was P. aeruginosa with sensitivities ranging from 20% to 80%, while Moraxella sp. represented the most sensitive pathogen with sensitivities ranging from 71.4% to 100%. Other bacterial isolates also elicited antibiotic sensitivities in the range of 33.3-100%. A total of 101 isolates were screened for plasmids, of which 45 harbored plasmids, yielding a plasmid frequency of 44.6%. Conjugal transfer of resistance to chloramphenicol, ampicillin, and streptomycin was detected in the transconjugants after the mating experiment. The antibiotic resistances were transferred either singly or in combination from six of the seven selected donor strains. The antibiotic resistance pattern transferred by these donor strains was partial and was associated with the transfer of R plasmids of sizes 21.3, 15.2, and 5.0 kb from three of the six transferable strains. The frequencies of transfer of antibiotype or R plasmids to the transconjugants ranged from 1.8 × 10(-7) to 1.4 × 10(-5) transconjugants per donor strain.

CONCLUSION

Conjunctivitis as an eye problem in Lagos is polymicrobial with infections associated with transferable R plasmids for chloramphenicol, ampicillin, and streptomycin. Continuous surveillance of conjunctivitis in relation to etiology, drug susceptibility, and plasmid transferability in the study area is therefore recommended.