Acute necrotic stomatitis (noma) associated with methicillin-resistant Staphylococcus aureus infection in a newly acquired rhesus macaque (Macaca mulatta)

Dynamics of Antimicrobial Resistance Carriage in Koalas (Phascolarctos Cinereus) and Pteropid Bats (Pteropus Poliocephalus) Before, During and After Wildfires

In the 2019-2020 summer, wildfires decimated the Australian bush environment and impacted wildlife species, including koalas (Phascolarctos cinereus) and grey headed flying fox pups (Pteropid bats, Pteropus poliocephalus). Consequently, hundreds of koalas and thousands of bat pups entered wildlife hospitals with fire-related injuries/illness, where some individuals received antimicrobial therapy. This study investigated the dynamics of antimicrobial resistance (AMR) in pre-fire, fire-affected and post-fire koalas and Pteropid bat pups. PCR and DNA sequencing were used to screen DNA samples extracted from faeces (koalas and bats) and cloacal swabs (koalas) for class 1 integrons, a genetic determinant of AMR, and to identify integron-associated antibiotic resistance genes. Class 1 integrons were detected in 25.5% of koalas (68 of 267) and 59.4% of bats (92 of 155). Integrons contained genes conferring resistance to aminoglycosides, trimethoprim and beta-lactams. Samples were also screened for blaTEM (beta-lactam) resistance genes, which were detected in 2.6% of koalas (7 of 267) and 25.2% of bats (39 of 155). Integron occurrence was significantly higher in fire-affected koalas in-care compared to wild pre-fire koalas (P < 0.0001). Integron and blaTEM occurrence were not significantly different in fire-affected bats compared to pre-fire bats (P > 0.05), however, their occurrence was significantly higher in fire-affected bats in-care compared to wild fire-affected bats (P < 0.0001 and P = 0.0488 respectively). The observed shifts of AMR dynamics in wildfire-impacted species flags the need for judicious antibiotic use when treating fire-affected wildlife to minimise unwanted selective pressure and negative treatment outcomes associated with carriage of resistance genes and antibiotic resistant bacteria.

Impact of human created environments in the pathogenic potential and antimicrobial resistance of staphylococci from wild neotropical primates in Brazil

The non-human primate (NHP) Leontopithecus rosalia is an endangered species native of Brazil and lives in forest fragments with different levels of contact with humans (natural, private and urban). Other NHPs - Callithrix spp. - were introduced by humans and co-exist and interact with the native species in these forests. To evaluate if living in or close to human-modified environments could constitute a risk for L. rosalia, we compared the prevalence, genetic background, antibiotic susceptibility and virulence gene content of staphylococci collected from the native and the introduced species from different forest fragments. We found that presence in human-dominated environments increased the colonization rate of L. rosalia with Mammaliicoccus sciuri (former Staphylococcus sciuri) from 18 % to 85 % (p = 0.0001) and of Callithrix spp with Staphylococcus aureus from 6 % to 100 % (p = 0.0001). According to molecular typing data obtained differences probably resulted from dissemination of these bacterial species from the invader NHP species and from humans. Changes in microbiota were paralleled by an increase in the prevalence of Panton-Valentine Leukocidin gene and in resistance to beta-lactams, macrolides and/or lincosamides as exposure to human environment increased. In particular, erythromycin resistance in S. aureus from Callithrix spp. increased from 0 % to 50 % and resistance rate to at least one antibiotic in coagulase-negative staphylococci species from L. rosalia increased from 13 % to 56 % (p = 0.0003). Our results showed that contact of native animal species with human-created environments increased the content of antimicrobial resistant and pathogenic bacteria on their commensal microbiota, which ultimately can impact on their health. IMPORTANCE: Endangered animal species are vulnerable to environmental alterations and human activities have been repeatedly identified as factors driving drastic changes in the natural landscape. It is extremely important to monitor changes in the environment surrounding protected species, because this could lead to early detection of any potential threats. In this study, we found that the contact of L. rosalia - a protected non-human primate from Brazil - with human environments is related to changes in their commensal microbiota. These included an increase in the number of pathogenic and antibiotic resistant bacteria, which have a higher potential to cause infections that are more difficult to treat. We provided evidence for the harmful impact human contact has on L. rosalia. Also, our results suggest that monitoring of commensal microbiota of protected animal species might be a useful way of sensing the risks of protected species to human exposure.

Bacterial Genotype, Carrier Risk Factors, and an Antimicrobial Stewardship Approach Relevant to Methicillin-resistant Staphylococcus aureus Prevalence in a Population of Macaques Housed in a Research Facility

Methicillin-resistant Staphylococcus aureus (MRSA) remains a significant problem for human and animal health and can negatively affect the health status of macaques and other nonhuman primates (NHP) in research colonies. However, few publications provide guidance on the prevalence, genotype, or risk factors for macaques with MRSA and even fewer on how to effectively respond to MRSA once identified in a population. After having a clinical case of MRSA in a rhesus macaque, we sought to determine the MRSA carrier prevalence, risk factors, and genotypes of MRSA in a population of research NHPs. Over a 6-wk period in 2015, we collected nasal swabs from 298 NHPs. MRSA was isolated from 28% (n = 83). We then reviewed each macaque's medical record for a variety of variables including animal housing room, sex, age, number of antibiotic courses, number of surgical interventions, and SIV status. Analysis of these data suggests that MRSA carriage is associated with the room location, age of the animal, SIV status, and the number of antibiotic courses. We used multilocus sequence typing and spa typing on a subset of MRSA and MSSA isolates to determine whether the MRSA present in NHPs was comparable with common human strains. Two MRSA sequence types were predominant: ST188 and a novel MRSA genotype, neither of which is a common human isolate in the United States. We subsequently implemented antimicrobial stewardship practices (significantly reducing antimicrobial use) and then resampled the colony in 2018 and found that MRSA carriage had fallen to 9% (26/285). These data suggest that, as in humans, macaques may have a high carrier status of MRSA despite low clinically apparent disease. Implementing strategic antimicrobial stewardship practices resulted in a marked reduction in MRSA carriage in the NHP colony, highlighting the importance of limiting antimicrobial use when possible.

International Harmonization of Nomenclature and Diagnostic Criteria (INHAND): Non-proliferative and Proliferative Lesions of the Non-human Primate (M. fascicularis)

The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions Project (www.toxpath.org/inhand.asp) is a joint initiative of the Societies of Toxicologic Pathology from Europe (ESTP), Great Britain (BSTP), Japan (JSTP) and North America (STP) to develop an internationally accepted nomenclature for proliferative and nonproliferative lesions in laboratory animals. The purpose of this publication is to provide a standardized nomenclature for classifying microscopic lesions observed in most tissues and organs from the nonhuman primate used in nonclinical safety studies. Some of the lesions are illustrated by color photomicrographs. The standardized nomenclature presented in this document is also available electronically on the internet (http://www.goreni.org/). Sources of material included histopathology databases from government, academia, and industrial laboratories throughout the world. Content includes spontaneous lesions as well as lesions induced by exposure to test materials. Relevant infectious and parasitic lesions are included as well. A widely accepted and utilized international harmonization of nomenclature for lesions in laboratory animals will provide a common language among regulatory and scientific research organizations in different countries and increase and enrich international exchanges of information among toxicologists and pathologists.

Prevalence of Methicillin-Resistant Staphylococcus aureus in Shrines

Methicillin-resistant Staphylococcus aureus (MRSA) infection in human beings and animals is concerning; it stands out as one of the leading agents causing nosocomial and community infections. Also, marginally increasing drug resistance in MRSA has limited therapeutic options. This study focuses on estimating the prevalence of MRSA in shrines, a place where human and animal interaction is frequent, sharing antibiotic-resistant bacteria, antibiotic-resistant genes, and diseases. A total of 120 environmental swabs were collected from targeted areas during the study period, March 2018 to May 2018. Staphylococcus aureus was identified by growth on mannitol salt agar (MSA), and MRSA by growth on mannitol salt agar containing 4 μg Oxacillin, Gram staining, and conventional biochemical test. Isolates of S. aureus were characterized by antibiotic susceptibility testing using the disc diffusion method. MRSA and methicillin-sensitive S. aureus (MSSA) proportion were 19% and 81%, respectively; a high rate of MRSA was observed in isolates from Thapathali (28.6%). MSSA isolates showed a high rate of resistance to erythromycin (64.7%). MRSA isolates were resistant to gentamicin (50%), cotrimoxazole (25%), erythromycin (50%), and ciprofloxacin (25%). The isolates were susceptible to linezolid (100%), clindamycin (100%), ciprofloxacin (75%), erythromycin (50%), tetracycline (100%), and cotrimoxazole (75%). Intermediate resistance was also found in gentamicin (50%). Of the 11 MSSA isolates that were erythromycin resistant and clindamycin sensitive, 6 (54.5%) showed the inducible clindamycin resistance (ICR) pattern and 2 MRSA isolates that were erythromycin resistant and clindamycin sensitive showed ICR pattern. Fifteen MSSA isolates were β-lactamase positive, whereas only two MRSA isolates showed β-lactamase production. There exists a minimal research work on infectious diseases that are shared between primates and animals. This study suggests the pervasiveness of MRSA/MSSA in the shrines, which may be a primary place for pathogen exchange between humans and primates.

Staphylococcus aureus Epidemiology in Wildlife: A Systematic Review

Staphylococcus aureus is a common bacterial colonizer of humans and a variety of animal species. Many strains have zoonotic potential, moving between humans and animals, including livestock, pets, and wildlife. We examined publications reporting on S. aureus presence in a variety of wildlife species in order to more cohesively review distribution of strains and antibiotic resistance in wildlife. Fifty-one studies were included in the final qualitative synthesis. The most common types documented included ST398, ST425, ST1, ST133, ST130, and ST15. A mix of methicillin-resistant and methicillin-susceptible strains were noted. A number of molecular types were identified that were likely to be found in wildlife species, including those that are commonly found in humans or other animal species (including livestock). Additional research should include follow-up in geographic areas that are under-sampled in this study, which is dominated by European studies.

Spontaneous meningoencephalitis by Staphylococcus aureus in an infant golden-headed lion tamarin (Leontopithecus chrysomelas)

Non-human primates are susceptible to many bacteria, some of which bear zoonotic potential. We report the pathologic features of spontaneous fulminating meningoencephalitis by Staphylococcus aureus in a captive infant golden-headed lion tamarin (Leontopithecus chrysomelas) from Brazil.

Carriage of Methicillin-resistant Staphylococcus aureus in a Colony of Rhesus (Macaca mulatta) and Cynomolgus (Macaca fascicularis) Macaques

Methicillin-resistant Staphylococcus aureus (MRSA) carriage and infection are well documented in the human and veterinary literature; however only limited information is available regarding MRSA carriage and infection in laboratory NHP populations. The objective of this study was to characterize MRSA carriage in a representative research colony of rhesus and cynomolgus macaques through a cross-sectional analysis of 300 animals. MRSA carriage was determined by using nasal culture. Demographic characteristics of carriers and noncarriers were compared to determine factors linked to increased risk of carriage, and MRSA isolates were analyzed to determine antimicrobial susceptibility patterns, staphylococcal chromosome cassette mec (SCCmec) type, and multilocus sequence type (ST). Culture results demonstrated MRSA carriage in 6.3% of the study population. Animals with greater numbers of veterinary or experimental interventions including antibiotic administration, steroid administration, dental procedures, and surgery were more likely to carry MRSA. Susceptibility results indicated that MRSA isolates were resistant to β-lactams, and all isolates were resistant to between 1 and 4 non β-lactam antibiotics. In addition, 73.7% of MRSA isolates were identified as ST188-SCCmec IV, an isolate previously observed in an unrelated population of macaques and 15.8% were ST3268-SCCmec V, which has only been described in macaques. A single isolate had a novel sequence type, ST3478, and carried SCCmec V. These results suggest that NHP-adapted strains of MRSA exist and highlight the emergence of antimicrobial resistance in laboratory NHP populations.

Staphylococcus aureus Infecting and Colonizing Experimental Animals, Macaques, in a Research Animal Facility

An outbreak of methicillin-resistant Staphylococcus aureus (MRSA) infections on the skin and soft tissues of experimental macaques in the vivarium of The Rockefeller University, New York, triggered this observational and interventional study. We screened 14 macaques in the colony (samples from head, nares, and rectum) and their housing (40 environmental surfaces) four times in 1 year, for S. aureus colonization or contamination, while implementing enhanced decolonization and decontamination procedures. A total of 114 isolates of S. aureus were recovered and characterized (antibiograms, spa typing, multilocus sequence typing, pulsed-field gel electrophoresis [PFGE], mecA, Panton-Valentine Leukocidin, and arginine catabolic mobile element). Based on these results, six strains of S. aureus were identified: two MRSA strains (t16708/ST3862/PFGE-A, t16709/ST3862/PFGE-C) and one methicillin-sensitive S. aureus (t8397/ST3884/PFGE-D) were characterized for the first time in this study; strains belonging to spa types t189 and t4167 have been identified in primates in previous studies. None of these strains was common to the neighboring New York City human community. Thus, it seems probable that the animals were already colonized upon arrival to the University. We suggest screening primates for S. aureus carriage upon arrival to University vivaria and possible implementation of extensive decolonization procedures before any surgical interventions.

Antibiotic resistance in Staphylococcus sp. isolated from the vaginal environment of squirrel monkeys (Saimiri spp.) bred ex situ

BACKGROUND

Squirrel monkeys (Saimiri spp.) have been widely used as animal models; however, the occurrence of Staphylococcus sp in their vaginal microbiota remains to be described.

METHODS

Samples were collected from 175 adult squirrel monkeys to isolate Staphylococcus sp and to test for susceptibility to a panel of nine antimicrobial agents.

RESULTS

Isolates with characteristics of the genus Staphylococcus were detected in 95 of 175 samples. Coagulase-negative staphylococci (CoNS) were the most common (95.8%, 91/95) isolates. Resistance to antibiotics was observed in 47.3% (45/95) of isolates. Resistance to tetracycline was observed in 28.5% (26/91), chloramphenicol in 15.4% (14/91), and methicillin in 13.2% (12/91) of CoNS. Coagulase-positive staphylococci were resistant to tetracycline, erythromycin, and methicillin.

CONCLUSIONS

The presence of Staphylococcus sp in vaginal samples obtained from squirrel monkeys suggests that these animals were in a carrier state. Furthermore, isolating strains resistant to methicillin reinforces the biosafety care of a colony.

Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing

Staphylococcus aureus is an important pathogen of humans and animals. We genome sequenced 90 S. aureus isolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions of S. aureus from humans to green monkeys (Chlorocebus sabaeus) in The Gambia over different time scales. We report a novel monkey-associated clade of S. aureus that emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission of S. aureus from monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens.

IMPORTANCE The population structures of Staphylococcus aureus in humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission of S. aureus between humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host.

Transmission of MDR MRSA between primates, their environment and personnel at a United States primate centre

OBJECTIVES

MDR MRSA isolates cultured from primates, their facility and primate personnel from the Washington National Primate Research Center were characterized to determine whether they were epidemiologically related to each other and if they represented common local human-associated MRSA strains.

METHODS

Human and primate nasal and composite environmental samples were collected, enriched and selected on medium supplemented with oxacillin and polymyxin B. Isolates were biochemically verified as Staphylococcus aureus and screened for the mecA gene. Selected isolates were characterized using SCCmec typing, MLST and WGS.

RESULTS

Nasal cultures were performed on 596 primates and 105 (17.6%) were MRSA positive. Two of 79 (2.5%) personnel and two of 56 (3.6%) composite primate environmental facility samples were MRSA positive. Three MRSA isolates from primates, one MRSA from personnel, two environmental MRSA and one primate MSSA were ST188 and were the same strain type by conventional typing methods. ST188 isolates were related to a 2007 ST188 human isolate from Hong Kong. Both MRSA isolates from out-of-state primates had a novel MLST type, ST3268, and an unrelated group. All isolates carried ≥1 other antibiotic resistance gene(s), including tet(38), the only tet gene identified.

CONCLUSIONS

ST188 is very rare in North America and has almost exclusively been identified in people from Pan-Asia, while ST3268 is a newly reported MRSA type. The data suggest that the primate MDR MRSA was unlikely to come from primate centre employees. Captive primates are likely to be an unappreciated source of MRSA.